[Correlation analysis of quality,origin and phenotypic characters of Paris polyphylla var. yunnanensis]

In order to provide guidance for the protection and utilization of resources,quality control and breeding of improved varieties,we compared the main phenotypic characters and quality of wild and transplanted Paris polyphylla var. yunnanensis collected from different producing areas. Seven phenotypic characters of 33 samples of P. polyphylla var. yunnanensis collected from Yunnan,Guizhou and Sichuan were determined by conventional methods,and the principal component analysis and cluster analysis were used to analyze the diversity of the samples. The parissaponin( polyphyllin Ⅰ,Ⅱ,Ⅵ,Ⅶ) content of the samples were detected by HPLC,and analyzed by cluster analysis. Correlation analysis of the phenotypic characters and the parissaponin content was performed. There were significant differences in seven phenotypic characters between wild and transplanted samples of P. polyphylla var. yunnanensis from different habitats,with high phenotypic diversity and abundant genetic variation. The results of principal component analysis showed that leaf shape index was the main factor of morphological variation of P. polyphylla var. yunnanensis. Cluster analysis showed that the phenotypic characters of wild and transplanted P. polyphylla var. yunnanensis could not be completely separated. The content of saponins in wild and transplanted samples from different habitats was quite different. Saponins content of 93. 94% samples met the criterion of Chinese Pharmacopoeia 2015 edition,and the overall quality was relatively steady. The results of independent sample t-test showed that there was no significant difference of all the active ingredient between wild and transplanted samples,and it couldn't be used to distinguish between wild and transplanted samples. It is the same as the results of cluster analysis. The results of correlation analysis showed that the phenotypic traits of P. polyphylla var. yunnanensis were correlated with its medicine quality,and the total content of saponins was positively correlated with leaf length and leaf shape index( r = 0. 389,0. 441; P<0. 05). Yunnan,Guizhou and Sichuan are suitable for the growth of P. polyphylla var. yunnanensis. And the transplaned P. polyphylla var. yunnanensis can be used as the same as the wild ones completely. The results provide reference for the protection and selective breeding of P. polyphylla var. yunnanensis.

Phenotypic Diversity Arises from Secondary Signal Loss in the Elaborate Visual Displays of Toucans and Barbets

Complexity and diversity are fundamental characteristics of life, but the relationship between the two remains murky. For example, both gaining and losing complexity can support diversity-so how exactly does complexity influence the emergence of unique phenotypes? Here we address this question by examining how complexity underlies the diversity of elaborate visual displays in the avian clade Ramphastides (toucans and barbets). These species communicate in part by using body movement and colorful ornaments on the tail. We find that sexual size dimorphism predicts the evolution of one specific signal, the tail-cock gesture, implying that tail cocking is more likely to evolve under stronger sexual selection. We also discover process-level constraints on the evolution of complexity: signals are gained along a strict order of operations, where the tail-cock gesture arises before other colors and gestures. Yet virtually any signal can be lost at any time. As a result, many extant phenotypes were more likely to arise through loss of complexity, highlighting the importance of secondary signal loss to phenotypic diversity. Collectively, our results demonstrate how sexual selection catalyzes the evolution of complex phenotypes, which indirectly support diversity by allowing different traits to be modified or lost in the future.

Assessing the utility of conserving evolutionary history

It is often claimed that conserving evolutionary history is more efficient than species‐based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human‐centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile.

Most – but not all – arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity–ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here.

The fitness cost and benefit of phase-separated protein deposits

Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase-separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can influence cell-to-cell variation in free protein abundance between individuals of a cell population (i.e., gene expression noise). This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase-separated assemblies and may influence cell fitness.

The Divergent Genomes of Teleosts

Boasting nearly 30,000 species, teleosts account for half of all extant vertebrates and approximately 98% of all ray-finned fish species (Actinopterygii). Teleosts are also the largest and most diverse group of vertebrates, exhibiting an astonishing level of morphological, physiological, and behavioral diversity. Previous studies had indicated that the teleost lineage has experienced an additional whole-genome duplication event. Recent comparative genomic analyses of teleosts and other bony vertebrates using spotted gar (a nonteleost ray-finned fish) and elephant shark (a cartilaginous fish) as outgroups have revealed several divergent features of teleost genomes. These include an accelerated evolutionary rate of protein-coding and nucleotide sequences, a higher rate of intron turnover, loss of many potential cis-regulatory elements and shorter conserved syntenic blocks. A combination of these divergent genomic features might have contributed to the evolution of the amazing phenotypic diversity and morphological innovations of teleosts.

Successive Paradigm Shifts in the Bacterial Cell Cycle and Related Subjects

A paradigm shift in one field can trigger paradigm shifts in other fields. This is illustrated by the paradigm shifts that have occurred in bacterial physiology following the discoveries that bacteria are not unstructured, that the bacterial cell cycle is not controlled by the dynamics of peptidoglycan, and that the growth rates of bacteria in the same steady-state population are not at all the same. These paradigm shifts are having an effect on longstanding hypotheses about the regulation of the bacterial cell cycle, which appear increasingly to be inadequate. I argue that, just as one earthquake can trigger others, an imminent paradigm shift in the regulation of the bacterial cell cycle will have repercussions or "paradigm quakes" on hypotheses about the origins of life and about the regulation of the eukaryotic cell cycle.

Phenotypic Parent Selection Within a Khorasan Wheat Collection and Genetic Variation in Advanced Breeding Lines Derived by Hybridization With Durum Wheat

Tetraploid relatives of durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husnot) represent an important reservoir of economically useful genes for development of new wheat cultivars. Two field experiments were conducted at Foggia (Italy), in the 2004 to 2006 and 2012 to 2015 growing seasons. In the first, 77 Khorasan wheat [T. turgidum subsp. turanicum (Jakubz.) Á. Löve & D. Löve] accessions from 23 countries of four geographic regions (Africa, Asia, Europe, and others) were evaluated to explore breeding opportunities. Seven agronomic traits were used to describe the diversity among the accessions: days to heading (HT), plant height (PH), grain yield (GY), specific weight (SW) as an indication of the density of the grain, 1000-grain weight (TGW), protein content, and gluten content. The total Shannon-Weaver diversity index was used to estimate phenotypic diversity, which ranged from monomorphic for PC (0.39) to highly polymorphic for TGW (0.67). A high level of total variation (87%) was attributed to the within-region diversity. The accessions grouped into six clusters, and seven elite accessions were selected as parents for crosses with durum wheat. In the second experiment, ten parents (seven Khorasan accessions and three durum wheat cultivars) and 790 F6 recombinant inbred lines (RILs) from the different T. durum × T. turgidum subsp. turanicum crosses were included to study genotypic and phenotypic variability of the same agronomic traits, plus the susceptibility index (SI) for disease. The genotypic coefficients of variation were lower than the phenotypic ones for all of the traits, which showed an environment effect on expression of these traits. High broad-sense heritability (h² _b > 86%) was recorded for all traits, and high h² _b coupled with high genetic gain as percentage of the mean (ΔG) was observed for HT, PH, GY, and SW, and for SI. This suggests that selection for these traits will provide good responses. Four principal components explained 70% of the total variation, and the genotypes were clustered into 20 groups. According to the results, some lines could be tested in varietal registration trials, and/or could be used as a significant breeding pool for durum wheat cultivar development in Mediterranean area.

The role of local adaptation in sustainable village chicken production

Village chickens are ubiquitous in smallholder farming systems, contributing to household, local and national economies under diverse environmental, economic and cultural settings. However, they are raised in challenging environments where productivity is low while mortality is high. There is much interest in utilizing indigenous genetic resources to produce a chicken resilient to its environment, whilst providing the basis of an economically sustainable enterprise. Globally, however, a wide variety of interventions have so far proved unable to deliver sustainable improvements. Here, we show that regional differences in trait preferences and parasite burden are associated with distinct chicken genepools, likely in response to interacting natural and human-driven (economic and social) selection pressures. Drivers of regional differences include marketing opportunities, cultural preferences, agro-ecologies and parasite populations, and are evident in system adaptations, such as management practices, population dynamics and bird genotypes. Our results provide sound multidisciplinary evidence to support previous observations that sustainable poultry development interventions for smallholder farmers, including breeding programs, should be locally tailored and designed for flexible implementation.

Saccharomyces interspecies hybrids as model organisms for studying yeast adaptation to stressful environments

The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes. Such fusing usually results in a wide variety of alterations at the genetic and chromosomal levels. The observed changes have suggested a high genome plasticity and a significant role of interspecies hybridization in the adaptation of yeasts to environmental stresses and industrial processes. There is a high probability that harsh wine and beer fermentation environments, from which the majority of interspecies hybrids have been isolated so far, influence their selection and stabilization as well as their genomic and phenotypic heterogeneity. The lessons we have learned about geno- and phenotype plasticity and the diversity of natural and commercial yeast hybrids have already had a strong impact on the development of artificial hybrids that can be successfully used in the fermentation-based food and beverage industry. The creation of artificial hybrids through the crossing of strains with desired attributes is a possibility to obtain a vast variety of new, but not genetically modified yeasts with a range of improved and beneficial traits. Copyright © 2017 John Wiley & Sons, Ltd.

Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass, Zostera marina

Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (FST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured "master" traits (like body size) might provide good predictions of overall trait differentiation.

[Community structure and leaf trait diversity in a vulnerable species, Phoebe chekiangensis (Lauraceae).]

Phoebe chekiangensis, as one original species of 'Nanmu with golden tint', harbors limited natural distribution regions, which is recognized as a vulnerable species in China under nationwide protection. Under the background of global climate change, it is of scientific significance to study the community structure and diversity of the natural populations of P. chekiangensis. In this study, community structure, species diversity and the phenotypic variation leaf traits in the communities of thirteen residue natural populations were analyzed. A total of 235 vascular species from 162 genera and 87 families were found in 16 plots within 13 natural populations, including 221 seed plants from 151 genera and 79 families. The species diversity in tree layer of community in Kaihua, Zhejiang and Linan, Zhejiang was significantly lower than that of other communities due to severe disturbance, while intermediate disturbance promoted the species diversity of shrub layer in community in Jianning, Fujian, and slight disturbance was beneficial to natural regeneration of P. chekiangensis. Foliage phenotype was important for species identification within Phoebe genus. There existed substantial variation in foliage phenotypic diversity among and within populations. The mean coefficient of variation was 17.2%, ranging from 10.4% to 27.5%. The variation was greater among populations (53.6%) than within populations (17.0%). Mean phenotypic differentiation coefficient was 75.1% among populations, indicating that the variance among populations was the main source for the phenotypic variation of the species. Results from the cluster analysis indicated that the 13 natural populations were divided into two distinct groups based on the Euclidean distance (10 cm), with stochastic variation.

Setting the bar

Analyzing the genomes of rock pigeons demonstrates that genetic variation comes in many forms and can have unexpected origins.

Parasitism and the Biodiversity-Functioning Relationship

Species interactions can influence ecosystem functioning by enhancing or suppressing the activities of species that drive ecosystem processes, or by causing changes in biodiversity. However, one important class of species interactions - parasitism - has been little considered in biodiversity and ecosystem functioning (BD-EF) research. Parasites might increase or decrease ecosystem processes by reducing host abundance. Parasites could also increase trait diversity by suppressing dominant species or by increasing within-host trait diversity. These different mechanisms by which parasites might affect ecosystem function pose challenges in predicting their net effects. Nonetheless, given the ubiquity of parasites, we propose that parasite-host interactions should be incorporated into the BD-EF framework.

Phenotype inference in an Escherichia coli strain panel

Understanding how genetic variation contributes to phenotypic differences is a fundamental question in biology. Combining high-throughput gene function assays with mechanistic models of the impact of genetic variants is a promising alternative to genome-wide association studies. Here we have assembled a large panel of 696 Escherichia coli strains, which we have genotyped and measured their phenotypic profile across 214 growth conditions. We integrated variant effect predictors to derive gene-level probabilities of loss of function for every gene across all strains. Finally, we combined these probabilities with information on conditional gene essentiality in the reference K-12 strain to compute the growth defects of each strain. Not only could we reliably predict these defects in up to 38% of tested conditions, but we could also directly identify the causal variants that were validated through complementation assays. Our work demonstrates the power of forward predictive models and the possibility of precision genetic interventions.

Multiple dimensions of intraspecific diversity affect biomass of eelgrass and its associated community

Genetic diversity within key species can play an important role in the functioning of entire communities. However, the extent to which different dimensions of diversity (e.g., the number of genotypes vs. the extent of genetic differentiation among those genotypes) best predicts functioning is unknown and may yield clues into the different mechanisms underlying diversity effects. We explicitly test the relative influence of genotypic richness and genetic relatedness on eelgrass productivity, biomass, and the diversity of associated invertebrate grazers in a factorial field experiment using the seagrass species, Zostera marina (eelgrass). Genotypic richness had the strongest effect on eelgrass biomass accumulation, such that plots with more genotypes at the end of the experiment attained a higher biomass. Genotypic diversity (richness + evenness) was a stronger predictor of biomass than richness alone, and both genotype richness and diversity were positively correlated with trait diversity. The relatedness of genotypes in a plot reduced eelgrass biomass independently of richness. Plots containing eelgrass with greater trait diversity also had a higher abundance of invertebrate grazers, while the diversity and relatedness of eelgrass genotypes had little effect on invertebrate abundance or richness. Our work extends previous findings by explicitly relating genotypic diversity to trait diversity, thus mechanistically connecting genotypic diversity to plot-level yields. We also show that other dimensions of diversity, namely relatedness, influence eelgrass performance independent of trait differentiation. Ultimately, richness and relatedness captured fundamentally different components of intraspecific variation and should be treated as complementary rather than competing dimensions of biodiversity affecting ecosystem functioning.

Natural mismatch repair mutations mediate phenotypic diversity and drug resistance in Cryptococcus deuterogattii

Pathogenic microbes confront an evolutionary conflict between the pressure to maintain genome stability and the need to adapt to mounting external stresses. Bacteria often respond with elevated mutation rates, but little evidence exists of stable eukaryotic hypermutators in nature. Whole genome resequencing of the human fungal pathogen Cryptococcus deuterogattii identified an outbreak lineage characterized by a nonsense mutation in the mismatch repair component MSH2. This defect results in a moderate mutation rate increase in typical genes, and a larger increase in genes containing homopolymer runs. This allows facile inactivation of genes with coding homopolymer runs including FRR1, which encodes the target of the immunosuppresive antifungal drugs FK506 and rapamycin. Our study identifies a eukaryotic hypermutator lineage spread over two continents and suggests that pathogenic eukaryotic microbes may experience similar selection pressures on mutation rate as bacterial pathogens, particularly during long periods of clonal growth or while expanding into new environments.

As humans, we often think of genetic mutations as being bad. Over the past several decades we have seen health warnings issued on a variety of environmental exposures, from cigarettes to tanning beds, and with good reason because they cause mutations. For multicellular organisms like humans, these mutations are strongly associated with cancer. But in bacteria, this is not true. In fact, the rate at which mutations occur sometimes increases to help bacteria cope with stressful environments.

Unlike bacteria, humans are eukaryotes – the name given to organisms whose cells contain different compartments separated by membranes, such as the nucleus of the cell. For years, we have assumed that eukaryotic microbes, like fungi and parasites, act more like humans than like bacteria because work in budding yeast (another eukaryote) has suggested this to be the case. However, recent work in disease-causing fungi has shown that, much like bacteria, elevated mutation rates may help them to respond to stress. This could also enable fungi to become resistant to drugs used to treat fungal infections.

Cryptococcus deuterogattii is a fungus that causes human diseases including meningoencephalitis and a lung infection called pulmonary cryptococcosis. An ongoing outbreak of the fungus began in the Pacific Northwest of Canada in the late 1990s and emerged in the United States in 2006/2007. Among isolates closely related to those fungi causing the outbreak, three were found that appear to have a specific mutation in their DNA mismatch repair pathway, meaning that they may also experience a higher mutation rate. These strains are also less able to cause disease than others.

Billmyre et al. now demonstrate experimentally that all three isolates have a specific DNA mismatch repair defect, and show that these fungi experience elevated mutation rates, resulting in what is known as a hypermutator state. Furthermore, whole genome sequencing and phylogenetic analysis showed that these hypermutator strains are derived from the outbreak-causing fungi, and that their reduced ability to cause disease is likely a result of accumulating mutations and the loss of the ability to grow at the higher temperatures found in the human body.

Fungal infections are difficult to treat, in part because there are a limited number of available drugs. Elevated mutation rates will likely increase how often and how rapidly fungi develop resistance to these drugs. Understanding how commonly fungi exhibit a hypermutator state that could impact the development of drug resistance will therefore be important for treating patients with fungal infections, which account for millions of infections and hundreds of thousands of deaths annually worldwide.

High prevalence of severe asthma in a large random population study

BACKGROUND

The prevalence of asthma severity is not well described at a population level.

OBJECTIVE

We sought to determine the prevalence of phenotypic signs of asthma severity among asthmatic patients in a general population and to describe risk factors for asthma severity.

METHODS

We performed an epidemiologic study conducted between 2008 and 2012 (West Sweden Asthma Study). A postal questionnaire was sent to a random population (n = 30,000) in west Sweden, with 18,087 responses. A total of 2,006 subjects were carefully phenotyped. Only subjects with "active asthma" (symptoms or medication in the last year, n = 744) were analyzed in this study to determine the degree of severity of the disease within an asthma cohort. Phenotypes of severity were calculated based on (1) multiple symptoms during the day despite ongoing use of asthma medications, (2) FEV₁ of less than 70% of predicted value, (3) daily or almost daily use of rescue medications, (4) nighttime symptoms once a week or more, and (5) oral corticosteroid use/emergency department visits. Asthmatic patients were grouped as having nonsevere disease, 1 sign of severity, or 2 or more signs of severity.

RESULTS

A total of 36.2% of asthmatic patients expressed at least 1 sign of asthma severity, and 13.2% had 2 or more signs. The group with 2 or more signs was older in age and had higher body mass index, a higher rate of tobacco smoking, and lower lung function. Bronchial hyperreactivity, airway inflammation, and sensitization were significantly different among the 3 groups. At a population level, the prevalence of asthma severity was 3.1% for 1 sign and 1.3% for at least 2 signs.

CONCLUSION

More than 1 in 3 asthmatic patients show at least 1 sign of asthma severity. The phenotypes of asthma severity are highly diverse, which is important to consider when implementing personalized medicine in asthmatic patients.

Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice

Allopolyploidization, that is, concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genomewide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock." However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain underinvestigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic and homoeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed generation (S5). We show that hybridization and whole genome duplication (WGD) have opposing effects on allelic and homoeologous expression in the F1 hybrids and tetraploids, respectively. Whereas hybridization exerts strong attenuating effects on allelic expression differences in diploid hybrids, WGD augments the intrinsic parental differences and generates extensive and variable homoeolog content which triggers diversification in expression patterning among the tetraploid plants. Coupled with the vast phenotypic diversity observed among the tetraploid individuals, our results provide experimental evidence in support of the notion that allopolyploidy catalyses rapid phenotypic diversification in higher plants. Our data further suggest that largely stochastic homoeolog content reshuffling rather than alteration in total expression level may be an important feature of evolution in young segmental allopolyploids, which underlies rapid expression diversity at the population level.

Candida albicans isolates from a single hospital show low phenotypical specialization

Candida albicans is the best-studied opportunistic human pathogenic yeast species, and its virulence factors, susceptibility to antimycotics, the diversity of its physiological properties and the determinative factors of these traits are interesting from a clinical as well as from an evolutionary perspective. By applying statistical modeling for the phenotypical differences observed among a collection of 63 C. albicans isolates originating from different clinical care units, from a diverse group of patients with or without mycosis, collected in a Hungarian clinic, we found that (i) host-related aspects like anatomical source, care unit of isolation, patients' age, sex, and disease severity, or ABC genotypes of the isolates had less effect on the phenotypic features of this opportunistic pathogen than host-independent aspects, for example, year or month of isolation; (ii) different phenotypic traits did not show any significant correlations with each other; and (iii) different genotypes displayed no anatomical specialization and rarely showed any significant correlation with parameters of isolation either. These results shed light on the dynamic nature and low specialization of the C. albicans populations observable in a narrow geographic range, namely in the patients hospitalized in the different care units of the clinic.

Allometric trajectories of body and head morphology in three sympatric Arctic charr (Salvelinus alpinus (L.)) morphs

A study of body and head development in three sympatric reproductively isolated Arctic charr (Salvelinus alpinus (L.)) morphs from a subarctic lake (Skogsfjordvatn, northern Norway) revealed allometric trajectories that resulted in morphological differences. The three morphs were ecologically assigned to a littoral omnivore, a profundal benthivore and a profundal piscivore, and this was confirmed by genetic analyses (microsatellites). Principal component analysis was used to identify the variables responsible for most of the morphological variation of the body and head shape. The littoral omnivore and the profundal piscivore morph had convergent allometric trajectories for the most important head shape variables, developing bigger mouths and relatively smaller eyes with increasing head size. The two profundal morphs shared common trajectories for the variables explaining most of the body and head shape variation, namely head size relative to body size, placement of the dorsal and pelvic fins, eye size and mouth size. In contrast, the littoral omnivore and the profundal benthivore morphs were not on common allometric trajectories for any of the examined variables. The findings suggest that different selective pressures could have been working on traits related to their trophic niche such as habitat and diet utilization of the three morphs, with the two profundal morphs experiencing almost identical environmental conditions.

Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding

Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomycescerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies.

FGFR2 mutation in a Chinese family with unusual Crouzon syndrome

AIM

To describe the clinical characteristics with genetic lesions in a Chinese family with Crouzon syndrome.

METHODS

All five patients from this family were included and received comprehensive ophthalmic and systemic examinations. Direct sequencing of the FGFR2 gene was employed for mutation identification. Crystal structure analysis was applied to analyze the structural changes associated with the substitution.

RESULTS

All patients presented typical Crouzon features, including short stature, craniosynostosis, mandibular prognathism, shallow orbits with proptosis, and exotropia. Intrafamilial phenotypic diversities were observed. Atrophic optic nerves were exclusively detected in the proband and her son. Cranial magnetic resonance imaging (MRI) implied a cystic lesion in her sellar and third ventricular regions. A missense mutation, FGFR2 p.Cys342Trp, was found as disease causative. This substitution would generate conformational changes in the extracellular Ig-III domain of the FGFR-2 protein, thus altering its physical and biological properties.

CONCLUSION

We describe the clinical presentations and genotypic lesions in a Chinese family with Crouzon syndrome. The intrafamilial phenotypic varieties in this family suggest that other genetic modifiers may also play a role in the pathogenesis of Crouzon syndrome.

Maintenance of phenotypic diversity within a set of virulence encoding genes of the malaria parasite Plasmodium falciparum

Infection by the human malaria parasite Plasmodium falciparum results in a broad spectrum of clinical outcomes, ranging from severe and potentially life-threatening malaria to asymptomatic carriage. In a process of naturally acquired immunity, individuals living in malaria-endemic regions build up a level of clinical protection, which attenuates infection severity in an exposure-dependent manner. Underlying this shift in the immunoepidemiology as well as the observed range in malaria pathogenesis is the var multigene family and the phenotypic diversity embedded within. The var gene-encoded surface proteins Plasmodium falciparum erythrocyte membrane protein 1 mediate variant-specific binding of infected red blood cells to a diverse set of host receptors that has been linked to specific disease manifestations, including cerebral and pregnancy-associated malaria. Here, we show that cross-reactive immune responses, which minimize the within-host benefit of each additionally expressed gene during infection, can cause selection for maximum phenotypic diversity at the genome level. We further show that differential functional constraints on protein diversification stably maintain uneven ratios between phenotypic groups, in line with empirical observation. Our results thus suggest that the maintenance of phenotypic diversity within P. falciparum is driven by an evolutionary trade-off that optimizes between within-host parasite fitness and between-host selection pressure.

The role of polyploidy in shaping morphological diversity in natural populations of Phlox amabilis

PREMISE OF THE STUDY

Studies of natural populations of polyploids increasingly highlight complex patterns of variation in ploidy and geographic distribution of cytotypes. As our understanding of the complexity of polyploidy grows, our understanding of the morphological correlates of polyploidy should expand as well. Here we examine in what ways, and to what degree, polyploidy affects the overall phenotype of a species across its distribution when there are three ploidies and geographic complexity in cytotype distribution.

METHODS

We measured 31 morphological traits from stems, leaves, and flowers from up to 25 individuals from 11 sites across the distribution of Phlox amabilis. Chromosome counts and flow cytometry confirmed and expanded upon earlier research documenting diploid, tetraploid, and hexaploid populations, and also identified a site with two ploidies. Univariate and multivariate statistics were used to characterize the morphological effects of polyploidy.

KEY RESULTS

We detected significant associations between morphology and ploidy in 11 traits spread across vegetative and reproductive structures. Generally, diploid individuals differed from polyploid individuals to a greater extent, and in different ways, than tetraploid and hexaploid plants differed from each other. Multivariate morphometrics demonstrated that the two primary axes of overall variation are driven by morphological traits associated with polyploidy, and individuals of different ploidies can be discriminated with 95% success.

CONCLUSIONS

Polyploidy plays a major role in shaping overall morphological diversity in natural populations of P. amabilis.

Coordination of cell decisions and promotion of phenotypic diversity in B. subtilis via pulsed behavior of the phosphorelay

The phosphorelay of Bacillus subtilis, a kinase cascade that activates master regulator Spo0A ~ P in response to starvation signals, is the core of a large network controlling the cell's decision to differentiate into sporulation and other phenotypes. This article reviews recent advances in understanding the origins and purposes of the complex dynamical behavior of the phosphorelay, which pulses with peaks of activity coordinated with the cell cycle. The transient imbalance in the expression of two critical genes caused by their strategic placement at opposing ends of the chromosome proved to be the key for this pulsed behavior. Feedback control loops in the phosphorelay use these pulses to implement a timer mechanism, which creates several windows of opportunity for phenotypic transitions over multiple generations. This strategy allows the cell to coordinate multiple differentiation programs in a decision process that fosters phenotypic diversity and adapts to current conditions.

The Power of Natural Variation for Model Organism Biology

Genetic background effects have long been recognized and, in some cases studied, but they are often viewed as a nuisance by molecular biologists. We suggest that genetic variation currently represents a critical frontier for molecular studies. Human genetics has seen a surge of interest in genetic variation and its contributions to disease, but insights into disease mechanisms are difficult since information about gene function is lacking. By contrast, model organism genetics has excelled at revealing molecular mechanisms of cellular processes, but often de-emphasizes genetic variation and its functional consequences. We argue that model organism biology would benefit from incorporating natural variation, both to capture how well laboratory lines exemplify the species they represent and to inform on molecular processes and their variability. Such a synthesis would also greatly expand the relevance of model systems for studies of complex trait variation, including disease.

Adaptive evolution in locomotor performance: How selective pressures and functional relationships produce diversity

Despite the complexity of nature, most comparative studies of phenotypic evolution consider selective pressures in isolation. When competing pressures operate on the same system, it is commonly expected that trade-offs will occur that will limit the evolution of phenotypic diversity, however, it is possible that interactions among selective pressures may promote diversity instead. We explored the evolution of locomotor performance in lizards in relation to possible selective pressures using the Ornstein-Uhlenbeck process. Here, we show that a combination of selection based on foraging mode and predator escape is required to explain variation in performance phenotypes. Surprisingly, habitat use contributed little explanatory power. We find that it is possible to evolve very different abilities in performance which were previously thought to be tightly correlated, supporting a growing literature that explores the many-to-one mapping of morphological design. Although we generally find the expected trade-off between maximal exertion and speed, this relationship surprisingly disappears when species experience selection for both performance types. We conclude that functional integration need not limit adaptive potential, and that an integrative approach considering multiple major influences on a phenotype allows a more complete understanding of adaptation and the evolution of diversity.

[Phenotypic and functional diversity of B lymphocytes]

For many years, it has been considered that the function of B cells is only to serve as precursors of antibody-producing plasma cells; however, this simplistic view has been challenged in the past thirty years. The first big surprise came during the seventies, when it was shown that B lymphocytes are not a homogeneous population, but is made up of various subpopulations with different origin and functions, including both innate and acquired immunity. During the eighties, it was discovered that B cells are an important source of cytokines, extending its functions from antigen presentation to cooperation with T cells. From the year two thousand, it is clear that B cells are, functionally speaking, as heterogeneous as T lymphocytes, extending its functions to the regulation of the immune response. The story does not end yet, as they continue to discover new features that will have to be incorporated into the main body of knowledge about the mechanisms by which the immune response works. Thus, we can conclude by congratulating the B lymphocytes by these first 50 years and we can predict at least another 50 of robust growth.

Morphological divergence between three Arctic charr morphs - the significance of the deep-water environment

Morphological divergence was evident among three sympatric morphs of Arctic charr (Salvelinus alpinus (L.)) that are ecologically diverged along the shallow-, deep-water resource axis in a subarctic postglacial lake (Norway). The two deep-water (profundal) spawning morphs, a benthivore (PB-morph) and a piscivore (PP-morph), have evolved under identical abiotic conditions with constant low light and temperature levels in their deep-water habitat, and were morphologically most similar. However, they differed in important head traits (e.g., eye and mouth size) related to their different diet specializations. The small-sized PB-morph had a paedomorphic appearance with a blunt head shape, large eyes, and a deep body shape adapted to their profundal lifestyle feeding on submerged benthos from soft, deep-water sediments. The PP-morph had a robust head, large mouth with numerous teeth, and an elongated body shape strongly related to their piscivorous behavior. The littoral spawning omnivore morph (LO-morph) predominantly utilizes the shallow benthic–pelagic habitat and food resources. Compared to the deep-water morphs, the LO-morph had smaller head relative to body size. The LO-morph exhibited traits typical for both shallow-water benthic feeding (e.g., large body depths and small eyes) and planktivorous feeding in the pelagic habitat (e.g., streamlined body shape and small mouth). The development of morphological differences within the same deep-water habitat for the PB- and PP-morphs highlights the potential of biotic factors and ecological interactions to promote further divergence in the evolution of polymorphism in a tentative incipient speciation process. The diversity of deep-water charr in this study represents a novelty in the Arctic charr polymorphism as a truly deep-water piscivore morph has to our knowledge not been described elsewhere.

Intraspecific facilitation by allelochemical mediated grazing protection within a toxigenic dinoflagellate population

Dinoflagellates are a major cause of harmful algal blooms (HABs), with consequences for coastal marine ecosystem functioning and services. Alexandrium fundyense (previously Alexandrium tamarense) is one of the most abundant and widespread toxigenic species in the temperate Northern and Southern Hemisphere and produces paralytic shellfish poisoning toxins as well as lytic allelochemical substances. These bioactive compounds may support the success of A. fundyense and its ability to form blooms. Here we investigate the impact of grazing on monoclonal and mixed set-ups of highly (Alex2) and moderately (Alex4) allelochemically active A. fundyense strains and a non-allelochemically active conspecific (Alex5) by the heterotrophic dinoflagellate Polykrikos kofoidii. While Alex4 and particularly Alex5 were strongly grazed by P. kofoidii when offered alone, both strains grew well in the mixed assemblages (Alex4 + Alex5 and Alex2 + Alex5). Hence, the allelochemical active strains facilitated growth of the non-active strain by protecting the population as a whole against grazing. Based on our results, we argue that facilitation among clonal lineages within a species may partly explain the high genotypic and phenotypic diversity of Alexandrium populations. Populations of Alexandrium may comprise multiple cooperative traits that act in concert with intraspecific facilitation, and hence promote the success of this notorious HAB species.

Adaptability of non-genetic diversity in bacterial chemotaxis

Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an alternative, or even evolutionary stepping-stone, to switching between multiple systems. We hypothesized that mutations in gene regulation could lead to heritable control of chemotactic diversity. By simulating foraging and colonization of E. coli using a single-cell chemotaxis model, we found that different environments selected for different behaviors. The resulting trade-offs show that populations facing diverse environments would ideally diversify behaviors when time for navigation is limited. We show that advantageous diversity can arise from changes in the distribution of protein levels among individuals, which could occur through mutations in gene regulation. We propose experiments to test our prediction that chemotactic diversity in a clonal population could be a selectable trait that enables adaptation to environmental variability.

DOI:http://dx.doi.org/10.7554/eLife.03526.001

Bacterial colonies are generally made up of genetically identical cells. Despite this, a closer look at the members of a bacterial colony shows that these cells can have very different behaviors. For example, some cells may grow more quickly than others, or be more resistant to antibiotics. The mechanisms driving this diversity are only beginning to be identified and understood.

Escherichia coli bacteria can move towards, or away from, certain chemicals in their surrounding environment to help them navigate toward favorable conditions. This behavior is known as chemotaxis. The signals from all of these chemicals are processed in E. coli by just one set of proteins, which control the different behaviors that are needed for the bacteria to follow them. Different numbers of these proteins are found in different—but genetically identical—bacteria, and the number of proteins is linked to how the bacteria perform these behaviors.

It has been suggested that diversity can be beneficial to the overall bacterial population, as it helps the population survive environmental changes. This suggests that the level of diversity in the population should adapt to the level of diversity in the environment. However, it remains unknown how this adaptation occurs.

Frankel et al. developed and combined several models and simulations to investigate whether differences in chemotaxis protein production help an E. coli colony to survive. The models show that in different environments, it can be beneficial for the population as a whole if different cells have different responses to the chemicals present. For example, if a lot of a useful chemical is present, bacteria are more likely to survive by heading straight to the source. If not much chemical is detected, the bacteria may need to move in a more exploratory manner.

Frankel et al. find that different amounts of chemotaxis proteins produce these different behaviors. To survive in a changing environment, it is therefore best for the E. coli colony to contain cells that have different amounts of these proteins. Frankel et al. propose that the variability of chemotaxis protein levels between genetically identical cells can change through mutations in the genes that control how many of the proteins are produced, and predict that such mutations allow populations to adapt to environmental changes.

The environments simulated in the model were much simpler than would be found in the real world, and Frankel et al. describe experiments that are now being performed to confirm and expand on their results. The model could be used in the future to shed light on the behavior of other cells that are genetically identical but exhibit diverse behaviors, from other bacterial species to more complex cancer cells.

DOI:http://dx.doi.org/10.7554/eLife.03526.002

Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice

Rice landraces are lineages developed by farmers through artificial selection during the long-term domestication process. Despite huge potential for crop improvement, they are largely understudied in India. Here, we analyse a suite of phenotypic characters from large numbers of Indian landraces comprised of both aromatic and non-aromatic varieties. Our primary aim was to investigate the major determinants of diversity, the strength of segregation among aromatic and non-aromatic landraces as well as that within aromatic landraces. Using principal component analysis, we found that grain length, width and weight, panicle weight and leaf length have the most substantial contribution. Discriminant analysis can effectively distinguish the majority of aromatic from non-aromatic landraces. More interestingly, within aromatic landraces long-grain traditional Basmati and short-grain non-Basmati aromatics remain morphologically well differentiated. The present research emphasizes the general patterns of phenotypic diversity and finds out the most important characters. It also confirms the existence of very unique short-grain aromatic landraces, perhaps carrying signatures of independent origin of an additional aroma quantitative trait locus in the indica group, unlike introgression of specific alleles of the BADH2 gene from the japonica group as in Basmati. We presume that this parallel origin and evolution of aroma in short-grain indica landraces are linked to the long history of rice domestication that involved inheritance of several traits from Oryza nivara, in addition to O. rufipogon. We conclude with a note that the insights from the phenotypic analysis essentially comprise the first part, which will likely be validated with subsequent molecular analysis.

Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries

Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra- and intermarket class crosses and introgressions of wild and cultivated Solanum relatives. To retrospectively explore the effects of potato breeding at the genome level, we used 8303 single-nucleotide polymorphism markers to genotype a 250-line diversity panel composed of wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011. Population structure analysis revealed four subpopulations within the panel, with cultivated potato lines grouping together and separate from wild species and genetic stocks. With pairwise kinship estimates clear separation between potato market classes was observed. Modern breeding efforts have scarcely changed the percentage of heterozygous loci or the frequency of homozygous, single-dose, and duplex loci on a genome level, despite concerted efforts by breeders. In contrast, clear selection in less than 50 years of breeding was observed for alleles in biosynthetic pathways important for market class-specific traits such as pigmentation and carbohydrate composition. Although improvement and diversification for distinct market classes was observed through whole-genome analysis of historic and current potato lines, an increased rate of gain from selection will be required to meet growing global food demands and challenges due to climate change. Understanding the genetic basis of diversification and trait improvement will allow for more rapid genome-guided improvement of potato in future breeding efforts.

Embryological-origin-dependent differences in homeobox expression in adult aorta: role in regional phenotypic variability and regulation of NF-κB activity

OBJECTIVE

Different vascular beds show differing susceptibility to the development of atherosclerosis, but the molecular mechanisms underlying these differences are incompletely understood. This study aims to identify factors that contribute to the phenotypic heterogeneity of distinct regions of the adult vasculature.

APPROACH AND RESULTS

High-throughput mRNA profiling in adult mice reveals higher expression of the homeobox paralogous genes 6 to 10 (Hox6-10) in the athero-resistant thoracic aorta (TA) than in the athero-susceptible aortic arch (AA). Higher homeobox gene expression also occurs in rat and porcine TA, and is maintained in primary smooth muscle cells isolated from TA (TA-SMCs) compared with cells from AA (AA-SMCs). This region-specific homeobox gene expression pattern is also observed in human embryonic stem cells differentiated into neuroectoderm-SMCs and paraxial mesoderm-SMCs, which give rise to AA-SMCs and TA-SMCs, respectively. We also find that, compared with AA and AA-SMCs, TA and TA-SMCs have lower activity of the proinflammatory and proatherogenic nuclear factor-κB (NF-κB) and lower expression of NF-κB target genes, at least in part attributable to HOXA9-dependent inhibition. Conversely, NF-κB inhibits HOXA9 promoter activity and mRNA expression in SMCs.

CONCLUSION

Our findings support a model of Hox6-10-specified positional identity in the adult vasculature that is established by embryonic cues independently of environmental factors and is conserved in different mammalian species. Differential homeobox gene expression contributes to maintaining phenotypic differences between SMCs from athero-resistant and athero-susceptible regions, at least in part through feedback regulatory mechanisms involving inflammatory mediators, for example, reciprocal inhibition between HOXA9 and NF-κB.

Replacing the first-generation dentition in pufferfish with a unique beak

Teleost fishes comprise approximately half of all living vertebrates. The extreme range of diversity in teleosts is remarkable, especially, extensive morphological variation in their jaws and dentition. Some of the most unusual dentitions are found among members of the highly derived teleost order Tetraodontiformes, which includes triggerfishes, boxfishes, ocean sunfishes, and pufferfishes. Adult pufferfishes (Tetraodontidae) exhibit a distinctive parrot-like beaked jaw, forming a cutting edge, unlike in any other group of teleosts. Here we show that despite novelty in the structure and development of this "beak," it is initiated by formation of separate first-generation teeth that line the embryonic pufferfish jaw, with timing of development and gene expression patterns conserved from the last common ancestor of osteichthyans. Most of these first-generation larval teeth are lost in development. Continuous tooth replacement proceeds in only four parasymphyseal teeth, as sequentially stacked, multigenerational, jaw-length dentine bands, before development of the functional beak. These data suggest that dental novelties, such as the pufferfish beak, can develop later in ontogeny through modified continuous tooth addition and replacement. We conclude that even highly derived morphological structures like the pufferfish beak form via a conserved developmental bauplan capable of modification during ontogeny by subtle respecification of the developmental module.

The inherited disorders of haemoglobin: an increasingly neglected global health burden

An estimated 300,000 babies are born each year with a severe inherited disease of haemoglobin and that over 80 per cent of these births occur in low- or middle-income countries. As these countries go through the epidemiological transition, characterized by a reduction in childhood and infant mortality due to improved public health measures, infants who had previously died of these conditions before they were recognised are now surviving to present for diagnosis and treatment. For a variety of reasons, even in the rich countries there are limited data about the true frequency, natural history, and survival of patients with these disorders, information that is absolutely critical towards providing governments and international health agencies with accurate information about the true global health burden of these conditions. The situation can only be improved by major action on the part of the rich countries together with the formation of partnerships between rich and poor countries and input from the major international health agencies and funding organisations.

Phenotypic diversity of Escherichia coli O157:H7 strains associated with the plasmid O157

Escherichia coli O157:H7, a food-borne pathogen, causes hemorrhagic colitis and the hemolytic-uremic syndrome. A putative virulence factor of E. coli O157:H7 is a 60-MDa plasmid (pO157) found in 99% of all clinical isolates and many bovine-derived strains. The well characterized E. coli O157:H7 Sakai strain (Sakai) and its pO157-cured derivative (Sakai-Cu) were compared for phenotypic differences. Sakai-Cu had enhanced survival in synthetic gastric fluid, did not colonize cattle as well as wild-type Sakai, and had unchanged growth rates and tolerance to salt and heat. These results are consistent with our previous findings with another E. coli O157:H7 disease outbreak isolate ATCC 43894 and its pO157-cured (43894-Cu). However, despite the essentially sequence identical pO157 in these strains, Sakai-Cu had changes in antibiotic susceptibility and motility that did not occur in the 43894-Cu strain. This unexpected result was systematically analyzed using phenotypic microarrays testing 1,920 conditions with Sakai, 43894, and the plasmid-cured mutants. The influence of the pO157 differed between strains on a wide number of growth/survival conditions. Relative expression of genes related to acid resistance (gadA, gadX, and rpoS) and flagella production (fliC and flhD) were tested using quantitative real-time PCR and gadA and rpoS expression differed between Sakai-Cu and 43894-Cu. The strain-specific differences in phenotype that resulted from the loss of essentially DNA-sequence identical pO157 were likely due to the chromosomal genetic diversity between strains. The O157:H7 serotype diversity was further highlighted by phenotypic microarray comparisons of the two outbreak strains with a genotype 6 bovine E. coli O157:H7 isolate, rarely associated with human disease.

Identification, Mefenoxam Sensitivity, and Compatibility Type of Phytophthora spp. Attacking Floriculture Crops in North Carolina

Phytophthora isolates were collected from floriculture crops grown in commercial greenhouses in North Carolina for species identification, compatibility type determination, and mefenoxam sensitivity tests. Isolation from 41 symptomatic plant species at 29 production locations resulted in 483 isolates from eight crops at seven locations. Phytophthora cryptogea (184 isolates) was recovered from dusty miller and gerbera daisy. All isolates of P. cryptogea were insensitive or intermediate in sensitivity to mefenoxam at 1 μg a.i./ml and were A1 compatibility type. P. nicotianae (273 isolates) was isolated from African violet, lavender, pansy, petunia, and vinca. Of these isolates, 21% were insensitive to mefenoxam at either 1 or 100 μg a.i./ml. Isolates of P. nicotianae from five locations were A2 compatibility type, whereas isolates on pansy at one location were A1 compatibility type. English ivy grown at two locations was infected with P. palmivora. All 26 isolates of P. palmivora were sensitive to mefenoxam and were A1 compatibility type. Mating type and mefenoxam sensitivity were uniform among isolates of P. nicotianae and P. palmivora from a given crop at a given location, suggesting that epidemics within a location may have originated from a single source of inoculum.

Spatial trends of phenotypic diversity between colonies of wild raspberry Rubus idaeus

• The question 'are fragmented wild populations of raspberry adaptively differentiated from each other and from cultivated forms of the same species?' is addressed here. • Plants collected from the coast, where commercial raspberries are grown, northwards by 49 km to an altitude of 600 m in Tayside, Scotland, were cultured in two common environments. Twenty phenotypic traits were recorded over 2 yr, on vegetative primocanes and then the single dominant floricane retained for year 2. A novel approach is presented for selecting traits that best discriminate between individuals using principal coordinate analysis. Phenotypic variation among accessions was then quantified using principal coordinate analysis followed by principal component analysis. • A consistent north-south trend was found. Plants from northern sites were shorter, bushier with less lateral growth and fewer flowers per lateral on the dominant fruiting cane. Plants from southern sites produced few, tall primocanes with greater cane diameters, lateral growth and flowering. The results were consistent across test environments. • The results confirm substantial, adaptive differentiation between populations and suggest a limited effect of cultivation on wild forms.