Genetic diversity of X-chromosome in populations of aboriginal Siberian ethnic groups: linkage disequilibrium structure and haplotype philogeography of ZFX locus

The structure of gene pool of the Siberian aboriginal population has been described based on the data on polymorphism of ZFX gene located on X-chromosome. In ten populations under study 49 haplotypes have been determined, three of which are presented with high frequency. Comparing the obtained results with the available data from HapMap project unique "African" haplotypes were revealed, which occurred in Yoruba population with the frequency of 3-7% and were not found in other populations. A coefficient of genetic differentiation of the Siberian ethnic groups under study amounted to 0.0486. Correlation analysis involving Mantel test did not reveal any significant correlations between a matrix of genetic distances and the matrices of geographic, linguistic and anthropological differences, where a maximum coefficient was obtained at the comparison with the anthropological matrix. Phylogenetic analysis proved strong isolation of African population from the other investigated ethnic groups. The Siberian populations were subdivided into two separate clusters: the first one included Yakuts, Buryats and Kets, while the second cluster included Altaians, Tuvinians and Khanty. A principal component analysis enabled to combine the investigated populations in three groups, which clearly differed by a degree of manifestation of Caucasoid and Mongoloid components. The first group included Europe inhabitants and one of Khanty populations, the second one--populations of South Siberia and China inhabitants. Mongoloid populations of East Siberia, the Japanese and Kets were combined in the third group. The results of barrier analysis revealed similar structure of genetic differentiation in the Siberian population. Linkage disequilibrium structure was obtained for six ethnic groups of Siberia. A unified linkage block by ten SNP of ZFX gene was found in five of the presented ethnic groups (excluding Ket population).     

The structure of the Polar Eskimo genealogy.

The structure of the genealogy of the Polar Eskimos from the Thule District of North Greenland is studied by a variety of computational and graphical means, some of them novel. It is shown that although the level of inbreeding in the population is low, the genealogy is intricately connected, as if conforming to the requirement that spouses are as unrelated as is possible in a small population.     

Spatial and temporal distribution patterns of flying Diptera

The temporal and spatial distributions of flying Diptera have been studied using suction traps hung at three levels and two distances from an emergent hedgerow tree. Most families were far more abundant in 1987 than in 1986, but patterns of spatial and temporal abundance were basically the same. Most families showed a marked concentration close to the tree. Scatopsidae accumulated away from the tree in large numbers. Most families concentrated at the mid-level, except the Anisopodidae and Mycetophilidae (top and bottom levels, respectively). Vertical distributions showed discontinuities for almost all families. It is suggested that the emergent hedgerow tree plays a very important part in the life of flying insects.     

Spatial and temporal predictions of moose winter distribution

Herbivores are usually distributed unevenly across the landscape often because of variation in resource availability. We used zero-inflated generalised additive models (to account for data with a high number of zeros) that include georeferences to predict winter distribution of a large herbivore (moose Alces alces). Moose distribution was analysed in relation to forage availability and distance to neighbouring sites. Our results showed that the ability to explain moose distribution indexed by pellet count data at a local scale increased when spatial information (longitude and latitude) was added to the model compared to the model only including food availability. By using the relationship between moose and forage distribution, and the spatial information, we predicted patch choice by moose reasonably well in 2 out of 4?years. However, the distribution of moose was also influenced by weather conditions, as it was most clumped in the year with most snow. In conclusion, our study lends support for a non-linear approach using georeferences for a comprehensive understanding of herbivore distribution at a small scale. This result also indicates that the use of a certain patch by moose not only depends on the selected patch itself but is also influenced by the neighbouring patch and factors at a larger spatial scale, such as moose management influencing the density above moose home range level. The relatively high proportion of unexplained variation suggests that the use of a certain patch is also influenced by other factors such as topography, predation, competition, weather conditions, and wildlife management strategies.     

Spatial and temporal distribution of copepod communities in the Adriatic Sea

The distribution of planktonic copepods in the Adriatic Seahas been analyzed on the basis of 132 samples collected at 35fixed stations during 4 seasonal cruises. A total of 127 specieshave been determined and 3 characteristic copepod communitieshave been identified. The distribution of copepod species hasbeen found to reflect the dual physiognomy of the Adriatic.The shallow northern section is characterized by high densityvalues, low species diversity, and the dominance of speciesbelonging to the estuarine and coastal communities. The relativelydeep waters of the southern section are characterized by lowdensity values, high species diversity, and the presence ofmany species belonging to the upper, middle, and lower zonesof the oceanic community. Temporal variations in the horizontalspread of these 3 communities are discussed in relation to seasonalcycles in abundance, vertical migration patterns, and the currentregime in the Adriatic.     

Spatial and temporal distribution patterns of Cladocera in the Argentine Sea

In the marine sciences, continuous monitoring systems have been regarded as very useful tools to provide continuous high frequency measurements of many parameters. We analyse here a high frequency time series of temperature measurements recorded every 10 min between 1997 and 2004 in the macro tidal Seine estuary (France) by a Marel buoy, an automatic monitoring network for littoral environment. We have adapted multi-scale data analysis methods to deal with the many missing values present in the time series. A power spectral density analysis is performed over time scales spanning 5 decades, from 20 min to more than 7 years. A scale invariant behaviour of the form with β = 2.2 is revealed for scales below 5 h. Over this scaling range, we have performed structure functions analysis, and shown that the Seine river temperature data exhibit turbulent-like intermittent properties, with multifractal statistics. The multifractal exponents obtained possess some similarities with passive scalar turbulence results. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Spatial and temporal population structure of Brevicoryne brassicae

Allozymes from individual aphids were used as markers to examine the structure of Brevicoryne brassicae colonies collected from field experiments at Horticulture Research International, Wellesbourne, during the summers of 1991, 1992 and 1993. Eighteen enzyme systems were examined using cellulose acetate electrophoresis, but only 6-phosphogluconate dehydrogenase (6-PGDH) showed polymorphism (three alleles) in the samples. There were significant differences in gene frequencies between populations at some sites within 1 kilometre and between times of sampling, with an increase in the proportion of the most common genotype AA later in the season, possibly due to selection during the summer of the best adapted clones. These changes in gene frequency might produce biased results in trials screening brassica crops against aphids.     

Spatial and temporal variability in the structure of a tropical forest

This study examines spatial and temporal variation in the forest structure of the Kibale National Park, Uganda by contrasting tree density, tree size, and forest composition among four areas each separated by less than 15 km, and by quantifying changes in the composition of one of these forests over a 20‐year period. Densities of some tree species differed markedly between sites, and some species common at one location were absent at others. Monthly phenological monitoring demonstrated that it was not uncommon for phenological patterns to differ between the forests. To examine temporal variation in the tree composition over a 20‐year period, a sampling regime that was carried out in the early 1970s was replicated on the floristic composition of one of these sites, using identical methods in the same sampling areas. While no form of human intervention occurred in this area between the early 1970s and 1992, there were marked changes in the densities of some tree species. Twenty‐seven percent of the identified species increased in abundance, 33% decreased, and 40% remained relatively unchanged. The observed spatial and temporal variation in forest composition could be the result of abiotic factors, such as altitude or rainfall, or biotic factors such as elephant and/or human influences on ecosystem dynamics; the implications of this variation for frugivores are discussed.     

Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay

The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay. By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a transect from the head to the mouth of the Chesapeake Bay during cruises in April and October 2001 and 2002. Standard curves for the quantitative PCR assays demonstrated that the relationship between gene copies and cycle threshold was linear and highly reproducible from 1 to 10(7) gene copies. The maximum number of 907h22 gene copies detected was approximately 140 ml(-1) and the maximum number of 912h4 gene copies detected was approximately 340 ml(-1). Sequence 912h4 was most abundant at the mouth of the Chesapeake Bay, and in general, its abundance increased with increasing salinity, with the highest abundances observed in April 2002. Overall, the 907h22 phylotype was most abundant at the mid-bay station. Additionally, 907h22 was most abundant in the April samples from the mid-bay and mouth of the Chesapeake Bay. Despite the fact that the Chesapeake Bay is rarely nitrogen limited, our results show that individual nitrogen-fixing bacteria have distinct nonrandom spatial and seasonal distributions in the Chesapeake Bay and are either distributed by specific physical processes or adapted to different environmental niches.     

Single-nucleotide polymorphisms and haplotype analysis in beta-defensin genes in different ethnic populations

Beta-defensins are cationic antimicrobial peptides expressed by epithelial cells and exhibit antibacterial, antifungal, and antiviral properties. The defensins are part of the innate host defense network and may have a significant protective role in the oral cavity and other mucosa. Defects or alteration in expression of the beta-defensins may be associated with susceptibility to infection and mucosal disorders. We examined the occurrence of single-nucleotide polymorphisms (SNPs) in the human beta-defensin genes DEFB1 and DEFB2 encoding human beta-defensin-1 and -2 (hBD-1, hBD-2), respectively, in five ethnic populations and defined haplotypes in these populations. Fifteen SNPs were identified in both DEFB1 and DEFB2. Coding region SNPs were found in very low frequency in both genes. One nonsynonymous DEFB1 SNP, G1654A (Val --> Ile), and one nonsynonymous DEFB2 SNP, T2312A (Leu --> His), were identified. Seven sites in each gene exhibited statistically significant differences in frequency between ethnic groups, with the greatest variation in the promoter and in the 5'-untranslated region of DEFB1. DEFB1 displayed 10 common haplotypes, including one cosmopolitan haplotype. Eight common haplotypes were found in DEFB2, including one cosmopolitan haplotype shared among all five ethnic groups. Our results show that genotypic variability among ethnic groups will need to be addressed when performing associative genetic studies of innate defense mechanisms and susceptibility to disease.     

PCR-based genotyping and haplotype analysis of human TCRBV gene segment polymorphisms

There are at least 63 tandemly arranged human T-cell receptor (Tcr) -chain variable region (BV) gene segments, which have presumably arisen by repeated gene duplication events. The 5-most half of the TCRBV gene loci is particularly complex in organization due to the presence of multiple interspersed members of the largest BV subfamilies, BV5, BV6, and BV13. Polymorphism and linkage relationships among these genes has been poorly characterized in part due to the high similarity of these duplicands. Germline DNA polymorphisms were specifically examined in the exons and introns of these and other BV gene segments distributed across 240 kilobases (kb) in this 5-most region. Polymerase chain reaction restriction enzyme-based assays were used to genotype ten point mutations in seven of the BV gene segments. Eight of these polymorphisms altered an amino acid of the BV gene segment. In addition, length polymorphisms due to simple sequence repeats were noted in the introns of six BV6 subfamily members. Approximately 250 unrelated haplotypes were constructed by segregation analyses of fifteen of these TCRBV polymorphisms. Linkage disequilibrium analyses indicated that haplotypic relationships are not detectable over a distance of more than 55 kb in this genomic region. These TCRBV polymorphisms, and the haplotypic analysis, provide important resources and guidance for future attempts to associate Tcr germline DNA differences in the human population with immune response differences, such as might occur in some autoimmune diseases.     

Spatial and temporal aspects of Gyrodinium galatheanum in Chesapeake Bay: distribution and mixotrophy

Gyrodinium galatheanum (Braarud) Taylor 1995 is a common bloom-forming,potentially toxic photosynthetic dinoflagellate in ChesapeakeBay, USA. Abundance of this dinoflagellate achieved densities>4 x 10³ cells ml^–1 in the mid- and upper Bay duringlate spring and early summer of 1995 and 1996. Ingestion ofcryptophytes by this dinoflagellate was detected in most samplescollected from the Bay. During late spring and early summer,mean number of ingested cryptophytes per G.galatheanum was ashigh as 0.46 for dinoflagellate populations located in surfacewaters of the mid- and upper Bay where dissolved inorganic phosphoruswas low. Observations on the distribution of G.galatheanum inChesapeake Bay show that populations of this dinoflagellatewere usually restricted to waters with salinities ranging from7 to 18 psu, seasonally progressed up the estuary, and usuallyco-occurred with cryptophytes. Correlation analysis indicatesthat abundance of G.galatheanum and incidence of feeding wasnegatively correlated with dissolved inorganic phosphorus, andthat incidence of feeding was positively correlated with abundanceof cryptophyte prey. These results indicate that G.galatheanumis an important component of the Chesapeake Bay phytoplanktonduring the spring and summer. Our results suggest that the phagotrophiccapability possessed by this phototrophic dinoflagellate maycontribute to its success in a varying-resource environmentlike Chesapeake Bay.     

Spatial and temporal determinants of genetic structure in Gentianella bohemica

The biennial plant Gentianella bohemica is a subendemic of the Bohemian Massif, where it occurs in seminatural grasslands. It has become rare in recent decades as a result of profound changes in land use. Using amplified fragment length polymorphisms (AFLP) fingerprint data, we investigated the genetic structure within and among populations of G. bohemica in Bavaria, the Czech Republic, and the Austrian border region. The aim of our study was (1) to analyze the genetic structure among populations and to discuss these findings in the context of present and historical patterns of connectivity and isolation of populations, (2) to analyze genetic structure among consecutive generations (cohorts of two consecutive years), and (3) to investigate relationships between intrapopulational diversity and effective population size (N(e)) as well as plant traits. (1) The German populations were strongly isolated from each other (pairwise F(ST)= 0.29-0.60) and from all other populations (F(ST)= 0.24-0.49). We found a pattern of near panmixis among the latter (F(ST)= 0.15-0.35) with geographical distance explaining only 8% of the genetic variance. These results were congruent with a principal coordinate analysis (PCoA) and analysis using STRUCTURE to identify genetically coherent groups. These findings are in line with the strong physical barrier and historical constraints, resulting in separation of the German populations from the others. (2) We found pronounced genetic differences between consecutive cohorts of the German populations (pairwise F(ST)= 0.23 and 0.31), which can be explained by local population history (land use, disturbance). (3) Genetic diversity within populations (Shannon index, H(Sh)) was significantly correlated with N(e) (R(S)= 0.733) and reflected a loss of diversity due to several demographic bottlenecks. Overall, we found that the genetic structure in G. bohemica is strongly influenced by historical periods of high connectivity and isolation as well as by marked demographic fluctuations in declining populations.     

Spatial and temporal variations in calanoid copepod distribution in the Straits of Malacca

The distribution and abundance of planktonic calanoid copepods were studied from samples collected at 13–20 stations during four oceanographic cruises (pre- and post- monsoons, and during northeast (NE) and southwest (SW) monsoons) performed between 1998 and 2000 in the Straits of Malacca. Space and time variations of calanoid copepods were described using univariate (number of species, diversity indices, abundance) as well as multivariate (MDS, ANOSIM, SIMPER) techniques from the Plymouth Routines in Multivariate Ecological Research (PRIMER) package. There were significant differences in abundance between the cruises. k-Dominance curves also revealed significant differences in the relative species abundance distributions among the monsoon periods, and a decrease in diversity from northern to southern parts of the Straits during each cruise. Multi-dimensional scaling revealed four groups of abundances with differences in species composition. Evidence from analysis of similarity (ANOSIM) suggested that the differences in communities among monsoon periods were significant, although spatial differences among samples in geographic locations in the northern, central and southern parts of the Straits were insignificant. These differences resulted from an overall change in the balance of relative abundance of few dominant species, rather from changes of many species. Similarity percentage analyses (SIMPER) indicated that the major species contributing to the average dissimilarity between monsoons varied temporally.     

Spatial and temporal distribution of the alkaloid sanguinarine in Sanguinaria canadensis L. (Bloodroot)

Acclimated and non-acclimated potted plants of Sanguinaria canadensis L. were harvested at early and late dormancy, anthesis, and immature and mature fruiting stages. Sanguinarine content and concentration were determined for rhizomes (distal, proximal, and middle sections), roots, leaves, flower, and fruit. Rhizomes had highest sanguinarine content and concentrations, and exhibited decreasing concentration gradients from the distal to proximal third. Concentrations in roots were a tenth of rhizome concentration. Concentrations in leaves, flowers, and fruit were one-thousandth of rhizome Sanguinarine content in whole acclimated plants was constant. Content in whole nonacclimated plants increased as the plant became physiologically active, but was constant during fruit maturation: content in roots, leaves, and fruit did not change. The substantial increase in whole-plant dry weight coupled with the unchanging sanguinarine content during fruit maturation suggests either a shift in photosynthate allocation from defense to growth, or a constant turnover of sanguinarine.     

Spatial and temporal depletion of haddock and pollack during the last century in the Kattegat‐Skagerrak

By reconstructing a centennial time‐series of stock spatio‐temporal dynamics and commercial landings, the long‐term erosion is shown of the spatial structure of haddock and pollack in the Skagerrak and Kattegat that resulted in their regional depletion in the area. The erosion occurred in parallel with the development of the industrial fisheries and the peak in landings was followed by a decline in adult biomass and individual size. Also found was that pollack adult biomass was significantly lower for elevated water temperatures, while the response for haddock was less clear. However the main decline of both stocks and the disappearance of their adult aggregations occurred several decades before the unprecedented warming trend, which started in the Skagerrak and Kattegat only in the mid‐1980s. These findings also suggest that haddock in the study area is not responding to the scale on which the management of the neighbouring North Sea haddock stock is currently performed. These results illustrate the hazardous consequences of prolonged overfishing on the population structure of commercially exploited stocks and the lack of knowledge which ultimately leads to spurious assumptions on the recovery potential of many fish stocks. Also argued is that the continuation of commercial fishery at ‘sustainable’ levels adjusted to the present stock productivity might hinder the recovery of these depleted stocks for a long period of time.     

Spatial and temporal distribution of sucrose synthase in the radish hypocotyl in relation to thickening growth.

Sucrose synthase (SuSy) is a key enzyme in the development of storage root of radish. Clarification of its spatial and temporal expression during the thickening growth of radish hypocotyl, which later develops into storage root, was carried out immunologically using light microscopy. Sequential harvests at 3, 7, 11 and 13 d after sowing (DAS) were performed on two radish cultivars having different sink capacity. A very low level of SuSy was observed 3 DAS for both cultivars. White Cherrish (WC; strong storage root) showed the maximum level of SuSy between 7 and 11 DAS with increased cell development (thickening), while in Kosena (K; low storage root) the level remained high after 13 d of growth. A high level of SuSy was found in companion cells, which was consistent with previous observations, but SuSy was also found in the xylem parenchyma and in some cortical cells. The level of SuSy differed according to the localization and depended highly on cell development. Both cell division and cell enlargement were stimulated in WC compared with K. The role of SuSy during thickening growth of radish hypocotyl is discussed in terms of utilizing photosynthates.     

Spatial and temporal distribution of Empoasca vitis within a vineyard

1 The intra‐plot spatial distribution of the green leafhopper Empoasca vitis (Goethe) (Cicadellidae, Empoascini) was assessed over three successive growing seasons in a Bordeaux vineyard. Weekly measurements of adult trappings and nymphal counts were performed in a 1.7‐ha plot on 130 sampling points. 2 Statistical and geostatistical analyses revealed inconsistent spatial distributions of adults and nymphs in spring, but consistent spatial distributions in summer, which were identical every year. 3 Similarities between spatial distributions of the mobile adults and the sedentary and aggregated nymphs strongly suggest that adults disperse inside the plot to areas preferred for egg deposition. 4 The similarity of summer populations among years suggests that this insects distribution is based on (perennial) differences in plot characteristics.     

夜郎湖水库水体不同形态汞的时空分布

于2006年7月(夏季)、2007年1月(冬季)和3月(春季)采集了贵州省夜郎湖水库水样,研究了不同形态汞(总汞、溶解态汞、颗粒态汞)的时空分布特征及其影响因素.结果表明,夏季水体总汞、溶解态汞、颗粒态汞平均含量分别为4.48±2.59、2.37±1.40、2.11±1.86 ng·L-1,均显著高于冬季和春季(P＜0.001),而冬春2季不同形态汞含量无明显差异.水质参数悬浮颗粒物(SPM)和硝酸盐(NO-3)与不同形态汞之间均存在显著的正相关关系,表明这些参数对于不同形态汞的季节分布起着重要作用.夏季农业耕作活动相对活跃,表层土壤的扰动增加,雨水冲刷农田土壤,带进大量的外源颗粒物,致使夜郎湖水体夏季总汞水平较高.空间分布表明,夜郎湖水库夏季总汞平均浓度从水库入库河流至大坝方向、出库河流呈现总体下降的分布趋势,但水体各采样剖面没有明显的分布规律.