Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Characterizing population structure using neutral markers is an important first step in association genetic studies in order to avoid false associations between phenotypes and genotypes that may arise from non-selective demographic factors. Population structure was studied in a wide sample of ∼1,300 coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] trees from Washington and Oregon. This sample is being used for association mapping between cold hardiness and phenology phenotypes and single-nucleotide polymorphisms in adaptive-trait candidate genes. All trees were genotyped for 25 allozyme and six simple sequence repeat (SSR) markers using individual megagametophytes. Population structure analysis was done separately for allozyme and SSR markers, as well as for both datasets combined. The parameter of genetic differentiation (θ or F _ST) was standardized to take into account high within-population variation in the SSR loci and to allow comparison with allozyme loci. Genetic distance between populations was positively and significantly correlated with geographic distance, and weak but significant clinal variation was found for a few alleles. Although the STRUCTURE simulation analysis inferred the same number of populations as used in this study and as based on previous analysis of quantitative adaptive trait variation, clustering among populations was not significant. In general, results indicated weak differentiation among populations for both allozyme and SSR loci (θ _s = 0.006–0.059). The lack of pronounced population subdivision in the studied area should facilitate association mapping in this experimental population, but we recommend taking the STRUCTURE analysis and population assignments for individual trees (Q-matrix) into account in association mapping.     

Analysing interspecific associations in parasites: alternative methods and effects of sampling heterogeneity

The purpose of the present study was (1) to test the ability of six alternative methods to detect random and non-random patterns of overall association in artificial presence/absence data sets, and (2) to analyse overall associations and effects of sampling heterogeneity in four empirical presence/absence data sets of helminths of the common shrew Sorex araneus. In the null model, the expected distribution was created by means of a randomisation procedure. Application of methods on artificial data sets indicated a generally low probability of type I statistical error. All methods were more likely to detect positive non-randomness than negative non-randomness of comparable strength, which may partly explain the predominance of positive overall associations in empirical data sets. The analyses based on artificial data sets indicated slight differences between methods in their ability to detect non-randomness of known strength (type II error). However, some of the methods failed to detect strong overall association when the artificial assemblages consisted of roughly equal numbers of positive and negative pairwise interactions. The structure of the artificial data sets always disappeared when the expected distribution was constrained to account for “sampling heterogeneity”, i.e. varying prevalence of species among subsamples. The patterns of overall association in real helminth communities were variable, depending on the locality and association method used, but not usually on the simulation constraint used. Of the four empirical data sets analysed, one showed an unequivocal positive structure, in one the structure depended on the method used, and two data sets from the same locality were unequivocally unstructured (random). We discuss the applicability of various association measures, and the possible causes of positive overall associations in parasites. Received: 20 October 1997 / Accepted: 4 May 1998     

The crystal structure of the calcium-bound con-G[Q6A] peptide reveals a novel metal-dependent helical trimer

The ability to form and control both secondary structure and oligomerization in short peptides has proven to be challenging owing to the structural instability of such peptides. The conantokin peptides are a family of γ-carboxyglutamic acid containing peptides produced in the venoms of predatory sea snails of the Conus family. They are examples of short peptides that form stable helical structures, especially in the presence of divalent cations. Both monomeric and dimeric conantokin peptides have been identified and represent a new mechanism of helix association, “the metallozipper motif” that is devoid of a hydrophobic interface between monomers. In the present study, a parallel/antiparallel three-helix bundle was identified and its crystal structure determined at high resolution. The three helices are almost perfectly parallel and represent a novel helix–helix association. The trimer interface is dominated by metal chelation between the three helices, and contains no interfacial hydrophobic interactions. It is now possible to produce stable monomeric, dimeric, or trimeric metallozippers depending on the peptide sequence and metal ion. Such structures have important applications in protein design.     

Species diversity and interspecific association in development sequence of Hippophae rhamnoides plantations in the Loess Hilly Region, China

Based on our field investigation, we analyzed the characteristics of species diversity and interspecific association at different development stages of Hippohae rhamnoides plantations. The results show that the species diversities of the shrub layer, grass layer and the whole community of the H. rhamnoides plantations all fluctuated in an “S” shape pattern. At different development stages, the species richness and diversity were higher in the grass layer than in the shrub layer. The shrub species diversity was lower on bare land, but increased gradually with development of the community. The shrub evenness index was higher in 13-year forest stand, while the grass diversity index was higher in the 3-year and 25-year plantations and lower in the 8-year plantation. The positive and negative absolute values of interspecific association between H. rhamonides and other principal species changed in a parabolic pattern. The significance level and intensity of interspecific association were lower or weaker in the13-year plantation, indicating that the species substitution rate slowed down, competition became less intense and community composition and its structure reached a relatively stable state. Therefore, to improve the ecological environment, priority should be given to the protection of the H. rhamnoides plantations younger than 13 years, while for those of 25 year plantations, moderate thinning should be made to promote their regeneration. __________ Translated from Chinese Journal of Applied Ecology, 2007, 18(1): 9–15 [译自: 应用生态学报]     

Effects of β2–microglobulin mutations on the alpha-1 helical region of H2-Ld

 Beta-2 microglobulin (β₂m)has been shown to have an effect on the structural and functional constraints that facilitate proper class I antigen presentation. To date, no evidence has pinpointed the β₂m-specific amino acids that play an integral role in affecting structure in and around the peptide binding region of class I. To delineate β₂m amino acid positions that affect the alpha-1 helical region, we generated a series of mutant β₂m proteins bearing precise amino acid substitutions. The amino acid positions chosen were based upon previous results which demonstrated that human β₂m association with H2-L^d altered the structure of the alpha-1/alpha-2 super-domain. β₂m mutant proteins were used in β₂m exchange assays with cells expressing H2-L^d. Following exchange, cells were assayed to determine whether mutant β₂m association resulted in structural alteration of class I extracellular domains. The alteration in H2-L^d structure was evidenced by an increase in the binding of an antibody (34-1-2), specific for the alpha-1 helical region of H2-L^d. Results demonstrated that amino acid substitutions in β₂m positions 33 and 53 led to a dramatic increase in the reactivity of the alpha-1 domain-specific antibody 34-1-2. Identifying β₂m amino acid positions that influence the structure of the peptide binding region may allow for a better understanding of cellular immune responses that center upon class I/β₂m expression. Received: 18 December 1997 / Revised: 19 February 1998     

The NMR structure of the domain II of a chloroplastic NifU-like protein OsNifU1A

NifU-like proteins are a highly conserved protein that serves as the scaffold for assembly of Fe-S clusters. Chloroplastic NifU-like proteins have tandem NifU like domains, named domain I and domain II. Although the amino acid sequences of these domains are very similar to each other, the predicted functional region for the Fe-S cluster assembly, the CXXC motif, exists only in domain I. The structure of the domain II of chloroplastic NifU-like protein OsNifU1A has an α-β sandwich structure containing two α helices located on one side of the β-sheet. The electrostatic surface potential of OsNifU1A domain II is predominantly positively charged. Chloroplastic NifU-like proteins are targeted to ferredoxin for transferring the Fe-S cluster. The ferredoxin presents an overall negatively charged surface, which may evoke an electrostatic association with OsNifU1A domain II.     

A Longitudinal Study of the Effects of Uncertainty on Reproductive Behaviors

Uncertainty exerts powerful influences on life history decisions. This has been demonstrated in experiments on nonhumans and in mathematical models. Studies of human populations are suggestive of the effects of uncertainty, but they rely on measures of environmental stress. In this paper, we derive a new measure of uncertainty, upsilon (υ), for use in non-experimental studies. We estimate its association with reproductive behaviors in a longitudinal panel sample of adolescents in the United States. Results show upsilon’s internal structure is consistent with theoretical models of uncertainty. Its associations with reproductive outcomes are also consistent with theoretical predictions. Upsilon seems to have its largest effect on the timing of fertility—increasing the odds of early fertility by a factor of 7, net of the effects of control variables. We discuss our findings for the association between υ and the timing of reproductive effort as well as our future research on υ.     

Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China

Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations are of great importance and the prerequisite for association mapping. In the present study, 145 genome-wide SSR markers were used to assess the genetic diversity, population structure, and LD of a set of 95 maize inbred lines which represented the Chinese maize inbred lines. Results showed that the population included a diverse genetic variation. A model-based population structure analysis subdivided the inbred lines into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Lancaster, Reid, Tangsipingtou and P. Among all of the inbred lines, 65.3% were assigned into the corresponding subgroups; others were assigned into a “mixed” subgroup. LD was significant at a 0.01 level between 63.89% of the SSR pairs in the entire sample and with a range of 18.75–40.28% in the subgroups. Among factors influencing LD, linkage was the major cause for LD of SSR loci. The results suggested that the population may be used in the detection of genome-wide SSR marker–phenotype association. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. R. Wang and Y. Yu contributed equally to the work.     

Linkage disequilibrium based association mapping of fiber quality traits in <Emphasis Type="Italic">G. hirsutum</Emphasis> L. variety germplasm

Cotton is the world’s leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r ² ≥ 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r ² ≥ 0.2 was reduced to ~5–6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at ‘moderate to strong’ and ‘strong to very strong’ evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Patterns of abundance and population structure of Pachycereus pringlei (Cactaceae), a columnar cactus of the Sonoran Desert

Understanding the mechanisms that determine the distribution and abundance of plants is a major problem in ecology. However, very few studies have explored the factors controlling the abundance of columnar cacti throughout their range of distribution. In this paper, we describe the density and size structure of 26 populations of Pachycereus pringlei throughout its distribution range in the Sonoran Desert. Major differences in abundance were detected between island and mainland and peninsular areas, with islands sustaining significantly larger densities than mainland and peninsular populations. Within peninsular populations, the abundance was negatively associated with latitude and positively associated with annual and seasonal rainfall. In contrast, the abundance in mainland populations showed neither latitudinal trend nor an association with rainfall. In peninsular populations, mean height and basal diameter of branched plants showed a negative association with population density whereas mainland populations showed no significant association. None of the populations exhibited a population structure that fitted the log-normal distribution expected for young, growing populations with constant recruitment. Insular, peninsular and␣mainland populations showed a population structure with an uneven size distribution typical of populations experiencing regeneration pulses.     

Insights into the structure of the LC13 TCR/HLA-B8-EBV peptide complex with molecular dynamics simulations

One key step in the immune response against infected or tumor cells is the recognition of the T-cell receptor (TCR) by class I major histocompatibility complexes. The complex between the HLA-B8 molecule and the immunodominant peptide with sequence FLRGRAYGL, derived from the Epstein-Barr virus, with the LC13 TCR has been determined by X-ray diffraction. The complex has been used as a starting point in a molecular dynamics study in order to investigate the dynamics of the complex association and to explore the specific interactions of the complex formation. The analyzed structures provided evidence that the peptide adopts an open type β-turn conformation close to C-terminal part, which dominates peptide/TCR interactions. Conformational energy landscape analysis indicated the presence of two conformational clusters in the peptide’s structure, underlying the backbone flexibility of the peptide despite being surrounded by two receptors. The peptide/MHC/TCR interface was found to hold significant number of solvent molecules, more specifically the peptide has been found to have approximately seventeen hydrogen bonds with water molecules. The molecular dynamics simulation indicated the disruption of some MHC/TCR contacts, mainly with the CDR1α loop. However, several other interactions emerged that resulted in a stable association during the 20 ns trajectory, as revealed by the buried surface area analysis.     

Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25–50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker–trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.     

The PNPase,exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

The structure and function of polynucleotide phosphorylase (PNPase) and the exosome, as well as their associated RNA-helicases proteins, are described in the light of recent studies. The picture raised is of an evolutionarily conserved RNA-degradation machine which exonucleolytically degrades RNA from 3′ to 5′. In prokaryotes and in eukaryotic organelles, a trimeric complex of PNPase forms a circular doughnut-shaped structure, in which the phosphorolysis catalytic sites are buried inside the barrel-shaped complex, while the RNA binding domains create a pore where RNA enters, reminiscent of the protein degrading complex, the proteasome. In some archaea and in the eukaryotes, several different proteins form a similar circle-shaped complex, the exosome, that is responsible for 3′ to 5′ exonucleolytic degradation of RNA as part of the processing, quality control, and general RNA degradation process. Both PNPase in prokaryotes and the exosome in eukaryotes are found in association with protein complexes that notably include RNA helicase.     

Genome-wide association study of bronchial asthma in the Volga-Urals region of Russia

Bronchial asthma is a chronic inflammatory respiratory disease caused by a complex interaction of environmental influences and genetic susceptibility. The first genome-wide association study of bronchial asthma discovered a significant association between single nucleotide polymorphisms (SNPs) located within the genomic region 17q12-q21 and childhood bronchial asthma in individuals of European descent. This result was later replicated in a number of independent population samples of European and Asian origin. Here we report the results of the first genome-wide association study of bronchial asthma in the Volga-Urals region of Russia. The study involved 358 unrelated patients with physician-diagnosed bronchial asthma and 369 disease-free control subjects of different ethnicity (Russians, Tatars, and Bashkirs). DNA specimens were genotyped using an Illumina Human610 quad array as a part of the GABRIEL project (EC contract no. LSHB-CT-2006-018996). After QC filtering procedures, a final set of 550 915 SNPs genotyped in 330 patients and 348 controls was tested for association with bronchial asthma. Five markers on chromosome 17q12-21 showed significant association with bronchial asthma (p ≤ 4.79 × 10⁻⁷). The rs7216389 SNP located in GSDMB intron 1 showed the strongest evidence for association (p = 1.01 × 10⁻⁷). Association with childhood asthma (p = 1.97 × 10⁻⁶ for rs7216389) was stronger than with late-onset asthma (p = 1.8 × 10⁻⁴ for rs7216389). A replication study of three SNPs located within GSDMB confirmed association only with childhood asthma. In sum, these results suggest that genetic variants of 17q12–q21 play an important role in susceptibility to bronchial asthma in the Volga-Urals region of Russia.     

Spatial structure of the abiotic environment and its association with sapling community structure and dynamics in a cloud forest

Analyzing the relationship between the spatial structures of environmental variables and of the associated seedling and sapling communities is crucial to understanding the regeneration processes in forest communities. The degree of spatial structuring (i.e., spatial autocorrelation) of environmental and sapling community variables in the cloud forest of Teipan, S Mexico, were analyzed at a 1-ha scale using geostatistical analysis; after fitting semivariogram models for each set of variables, the association between the two sets was examined through cross-variograms. Kriging maps of the sapling community variables (density, cover, species richness, and mortality and recruitment rates) were obtained through conditional simulation method. Canopy openness, total solar radiation, litter depth, soil temperature and soil moisture were spatially structured, as were sapling density, species richness and sapling mortality rate. Mean range in semivariograms for environmental and sapling community variables were 13.14 ± 3.67 and 12.68 ± 5.71 m (±SE), respectively. The spatial structure of litter depth was negatively associated with the spatial structures of sapling density, species richness, and sapling community cover; in turn, the spatial structure of soil moisture was positively associated with the spatial structure of recruitment rate. These associations of the spatial structures of abiotic and sapling community variables suggest that the regeneration processes in this cloud forest is driven by the existence of different microsites, largely characterized by litter depth variations, across which saplings of tree species encounter a range of opportunities for successful establishment and survival.     

A unique genome-wide association analysis in extended Utah high-risk pedigrees identifies a novel melanoma risk variant on chromosome arm 10q

Only two genome-wide association (GWA) screens have been published for melanoma (Nat Genet 47:920–925, 2009; Nat Genet 40:838–840, 2008). Using a unique approach, we performed a genome-wide association study in 156 related melanoma cases from 34 high-risk Utah pedigrees. Genome-wide association analysis was performed on nearly 500,000 markers; we compared cases to 2,150 genotypically matched samples from Illumina’s iControls database. We performed genome-wide association with EMMAX software, which is designed to account for population structure, including relatedness between cases. Three SNPs exceeded a genome-wide significance threshold of p < 5 × 10⁻⁸ on chromosome arm 10q25.1 (rs17119434, rs17119461, and rs17119490), where the most extreme p value was 7.21 × 10⁻¹². This study represents a new and unique approach to predisposition gene identification; and it is the first genome-wide association study performed in related cases in high-risk pedigrees. Our approach illustrates an example of using high-risk pedigrees for the identification of new melanoma predisposition variants.     

Maternal age and risk for trisomy 21 assessed by the origin of chromosome nondisjunction: a report from the Atlanta and National Down Syndrome Projects

We examined the association between maternal age and chromosome 21 nondisjunction by origin of the meiotic error. We analyzed data from two population-based, case–control studies: Atlanta Down Syndrome Project (1989–1999) and National Down Syndrome Project (2001–2004). Cases were live born infants with trisomy 21 and controls were infants without trisomy 21 delivered in the same geographical regions. We enrolled 1,215 of 1,881 eligible case families and 1,375 of 2,293 controls. We report four primary findings. First, the significant association between advanced maternal age and chromosome 21 nondisjunction was restricted to meiotic errors in the egg; the association was not observed in sperm or in post-zygotic mitotic errors. Second, advanced maternal age was significantly associated with both meiosis I (MI) and meiosis II (MII). For example, compared to mothers of controls, mothers of infants with trisomy 21 due to MI nondisjunction were 8.5 times more likely to be ≥40 years old than 20–24 years old at the birth of the index case (95% CI = 5.6–12.9). Where nondisjunction occurred in MII, mothers were 15.1 times more likely to be ≥40 years (95% CI = 8.4–27.3). Third, the ratio of MI to MII errors differed by maternal age. The ratio was lower among women <19 years of age and those ≥40 years (2.1, 2.3, respectively) and higher in the middle age group (3.6). Lastly, we found no effect of grand-maternal age on the risk for maternal nondisjunction. This study emphasizes the complex association between advanced maternal age and nondisjunction of chromosome 21 during oogenesis. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.     

Association of chromosome 8q24 variants with prostate cancer risk in the Siberian region of Russia and meta-analysis

Compelling evidence demonstrates the importance of chromosome 8q24 as a locus of susceptibility to prostate cancer. In this work, the association of common 8q24 variants, rs6983267 and rs1447295, with a sporadic risk of prostate cancer was analyzed in the Russian population of Siberia. For this purpose, the above polymorphisms were genotyped in 393 cases and 384 control individuals. The A allele of rs1447295 was significantly associated with prostate cancer risk (OR[CI 95%] = 1.74 [1.26–2.4], p = 7.8 × 10⁻⁴). The common G-A haplotype of rs6983267-rs1447295 also showed association with prostate cancer risk in Russians (OR[CI 95%] = 2.03 [1.1–3.75], p = 0.02). A meta-analysis combining our data with previously published results was performed to better evaluate the association between the SNPs studied and prostate cancer risk; its results strongly supported the association for both loci (p < 10⁻⁶). Thus, our study has confirmed the association of chromosome 8q24 with a risk of prostate cancer.     

Sp1 polymorphism in collagen I α1 gene is associated with osteoporosis in lumbar spine of Mexican women

The Sp1 binding site polymorphism in collagen type I alpha 1 gene (COLIA1) has been associated with osteoporosis (OP) and bone mineral density (BMD). The aim of this study was to explore the association of this polymorphism with OP and BMD in the Mexican population by polymerase chain reaction and restriction fragment length polymorphism (PCR–RFLP) procedure. Allelic and genotypic frequencies from the Sp1 polymorphism were determined in 100 women with OP, 100 women without OP and 500 subjects from general Mexican population (GMP). Distribution of Sp1 polymorphism was in Hardy–Weinberg equilibrium. In spite of population structure due to racial mix in Mexican population, associations with OP were demonstrated. The frequency of “s” allele was significantly higher in women with OP (35%) than in women without OP (11%; P < 0.00001). Interestingly, “ss” genotype, was exclusive of women with OP and was associated with low BMD (0.588 ± 0.077 g/cm²) in contrast to “SS” genotype (0.733 ± 0.039 g/cm²; P = 0.0001). This work confirms the association of Sp1 polymorphism with low BMD and OP in Mexican population and make sure to use Sp1 as a genetic marker for OP in our population.     

Seasonal variation of phytoplankton community structure and nitrogen uptake regime in the Indian Sector of the Southern Ocean

This study investigates the dynamics of phytoplankton communities and nitrogen uptake in the Indian sector of the Southern Ocean during spring and summer. The study area is oligotrophic (Chl a stocks <50 mg m⁻²); nevertheless, a large spatial variation of phytoplankton biomass and community structure was observed. During both seasons the phytoplankton community in the seasonal ice zone showed higher biomasses and was mainly composed of large diatom cells. However, in the permanently open ocean zone the community had low biomass and was chiefly composed of nano- and picoflagellates. In the polar front zone, although biomass was higher, the community structure was similar to the open ocean zone. The results suggest that the variation in phytoplankton community structure on a larger scale resonates with gradients in water column stability and nutrient distribution. However, significant changes in biomass and nutrient stocks but little change in community structure were observed. Absolute nitrogen uptake rates were generally low, but their seasonal variations were highly significant. During spring the communities displayed high specific nitrate uptake (mean rate = 0.0048 h⁻¹), and diatoms (in the seasonal ice zone) as well as nano- and picoflagellates (in the permanently open ocean zone and polar front zone) were mainly based on new production (mean ƒ-ratio = 0.69). The transition to summer was accompanied by a significant reduction in nitrate uptake rate (0.0048 h⁻¹ → 0.0011 h⁻¹) and a shift from predominantly new to regenerated production (ƒ-ratio 0.69 → 0.39). Ammonium played a major role in the seasonal dynamics of phytoplankton nutrition. The results emphasize that, despite a large contrast in community structure, the seasonal dynamics of the nitrogen uptake regime and phytoplankton community structure in all three subsystems were similar. Additionally, this study supports our previous conclusion that the seasonal shift in nitrogen uptake regime can occur with, as well as without, marked changes in community structure. Received: 2 December 1997 / Accepted: 20 April 1998