Genetic and demographic characteristics of rural populations of Altai Republic: Sex-Age composition,surname and tribal structure

The sex, age, tribal, and surname compositions of the populations of three villages of Altai Republic, Kulada (Ongudaisk raion), Beshpeltir (Chemal raion), and Kurmach-Baigol (Turochak raion) have been studied. Altaian populations are characterized by a high proportion of persons under 20 years of age (35.3–46.1%); however, there is a tendency towards a narrow base of the sex-age pyramid. The sex ratios in the total populations and in individual age groups are unfavorable. The rural populations studied differ in the spectrum and pattern of surname accumulation. The Kurmach-Baigol population (which consists of Northern Altaians) considerably differs from the Beshpeltir and Kulada populations (which are mostly Southern Altaian) with respect to the calculated parameters characterizing the population structure (random isonymy, migration index, the parameter of tribe diversity, entropy, and the redundancy of surname distribution). Isonymy coefficients of relationship between individual populations have been calculated from the data on tribes (surnames). These coefficients for pairs of populations are the following: for the Beshpeltir and Kulada populations, 0.3035938 (0.0000443 and 0.0000378 for the Altaian and total populations, respectively); for the Beshpeltir and Kurmach-Baigol populations, 0.0026788 (0.0000172 and 0.0000121 for the Altaian and total populations, respectively); and for the Kulada and Kurmach-Baigol populations, 0.0054811 (no common surnames have been found).Translated from Genetika, Vol. 41, No. 2, 2005, pp.254–260.Original Russian Text Copyright © 2005 by Kucher, Tadinova, Puzyrev.     

Delineating Europe's cultural regions: population structure and surname clustering

Surnames (family names) show distinctive geographical patterning and in many disciplines remain an underutilized source of information about population origins, migration and identity. This paper investigates the geographical structure of surnames, using a unique individual level database assembled from registers and telephone directories from 16 European countries. We develop a novel combination of methods for exhaustively analyzing this multinational data set, based upon the Lasker Distance, consensus clustering and multidimensional scaling. Our analysis is both data rich and computationally intensive, entailing as it does the aggregation, clustering and mapping of 8 million surnames collected from 152 million individuals. The resulting regionalization has applications in developing our understanding of the social and cultural complexion of Europe, and offers potential insights into the long and short-term dynamics of migration and residential mobility. The research also contributes a range of methodological insights for future studies concerning spatial clustering of surnames and population data more widely. In short, this paper further demonstrates the value of surnames in multinational population studies and also the increasing sophistication of techniques available to analyze them.     

Forest canopy structure analyzed by using aerial photographs

A method was developed using aerial photographs to analyze forest canopy structure. Digital elevation models of both the land and canopy surface in a mesh of 5 m intervals were made from aerial photographs taken in winter (without tree leaves) and summer (with leaves), respectively, in a 60 ha area of temperate deciduous forest. The difference between the two elevation values at each point was regarded as the canopy height, and a canopy height profile was constructed. The estimated canopy structure was compared with that obtained by ground observations in a 6 ha part of the study area. Large gaps (>100 m²) were adequately detected by the method, and the gap size distribution obtained was similar to the one observed on the ground. The method was found to be effective in analyzing the forest canopy structure of large areas, but it is not suitable for the detection of small gaps.     

Population structure and genetic diversity in insular populations of Nasutitermes takasagoensis (Isoptera: Termitidae) analyzed by AFLP markers

Dispersal ability and degree of inbreeding in a population can indirectly be assessed using genetic markers. In general, it was suggested that winged termites are not able to fly distances greater than several hundred meters. Here, amplified fragment length polymorphism (AFLP) was used to analyze genetic diversity, population substructure, and gene flow among insular populations of the termite Nasutitermes takasagoensis (Isoptera: Termitidae) in the Yaeyama Islands, Okinawa, Japan. Samples were collected from 77 nests on seven islands of the Yaeyama Group. Using three primer combinations a total of 155 bands were generated with 78 (50%) polymorphic bands. Genetic distance and G(st) values among insular populations were calculated. Relatively high genetic diversity and low values of G (st), suggest there is moderate subpopulation structure. Based on these results, we discussed two possibilities; first, winged termites are able to fly over distances of several kilometers, and second, these results were obtained because insular populations share a recent common origin.     

Developmental changes in rat liver mitochondrial populations analyzed by flow cytometry.

Isolated rat liver mitochondria were split into three density fractions when applied to a Percoll gradient. This phenomenon is observable in the fetus, in the early newborn (1 h), in the suckling newborn (7 days), and in the adult, suggesting that the three density fractions coexist regardless of the state of development. The medium-density fraction sharply decreased immediately after delivery, being replaced by the high-density fraction. Flow cytometry analysis of mitochondrial density fractions stained with rhodamine 123 showed the occurrence in each density fraction and in all developmental states studied of two distinct mitochondrial populations with different fluorescence intensities. Our results suggest that the high-fluorescence population might be an immature form of mitochondria that decreases with the progression of development, coinciding with the postnatal enhancement of mitochondrial respiratory efficiency.     

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

Alternative RNA splicing greatly expands the repertoire of proteins encoded by genomes. Next-generation sequencing (NGS) is attractive for studying alternative splicing because of the efficiency and low cost per base, but short reads typical of NGS only report mRNA fragments containing one or few splice junctions. Here, we used single-molecule amplification and long-read sequencing to study the HIV-1 provirus, which is only 9700 bp in length, but encodes nine major proteins via alternative splicing. Our data showed that the clinical isolate HIV-1_89.6 produces at least 109 different spliced RNAs, including a previously unappreciated ∼1 kb class of messages, two of which encode new proteins. HIV-1 message populations differed between cell types, longitudinally during infection, and among T cells from different human donors. These findings open a new window on a little studied aspect of HIV-1 replication, suggest therapeutic opportunities and provide advanced tools for the study of alternative splicing.     

Population structure of rural settlements of Sakha Republic (Yakutia): surname structure

The distributions of surnames have been studied in 12 rural ethnic territorial groups of Sakha Republic (Yakutia). The populations studied are characterized by considerable accumulation of individual surnames, the surname spectra of representative of different ethnic groups living in the same area substantially overlapping. The random isonymy, migration index, surname diversity, and the surname distribution redundancy index display geographic and ethnic differences. The isonymy relationship coefficients calculated for representatives of individual ethnic groups (Yakuts, Evens, and Russians) and for total populations of the settlements studied are determined by the geographic distances between the compared populations and the intensity of migrations.     

The border effect in surname structure: an Italian-Slovenian case study

Population surname structure in northeastern Italy municipalities, in which small Slovenian-speaking groups are present, are compared with neighboring populations of both Italian and Slovenian nationality. In the early 20th century those municipalities were part of the Italian territory and underwent a massive Italianization process that led to the mutation of the original Slovenian surnames into a derived Italian form. In order to track surname relationships among the examined communities, two different similarity analyses were performed: the first using the surnames as they are recorded in the Italian and Slovenian official telephone directories, and the second restoring the Italianized Slovenian surnames to their original form and then recalculating the populations' similarity. Both comparisons evidence a separation that depends on nationality, which is less marked after restoring surnames to their original form. Geographical elements, older historical events, and socioeconomic traits allow interpretation of these results.     

Lipophorin structure analyzed by in vitro treatment with lipases.

Adult Manduca sexta high density lipophorin (HDLp-A) is composed of three apolipoproteins (apoLp-I, -II, and -III) and 52% lipid. The flight-specific low density lipophorin (LDLp) contains 62% lipid and is associated with several additional molecules of apoLp-III. The amount of phospholipid remains constant in lipophorin (140 mol/mol of lipophorin), while the diacylglycerol content varies between different lipophorin species (310 mol/mol HDLp up to 1160 mol/mol LDLp). Both lipophorin particles were enzymatically depleted of phospholipid or diacylglycerol by in vitro incubation with either phospholipase A2 or triacylglycerol lipase. Albumin was used to remove free fatty acids generated during the reaction. Treatment with phospholipase A2 removed all phospholipids (except sphingomyelin) and the resulting particles were stable. Triacylglycerol lipase hydrolyzed large fractions of diacylglycerol. The resulting particles were smaller in size, higher in density, and devoid of apoLp-III. The particles retained apoLp-I and -II and the other lipid components, including a substantial amount of diacylglycerol. Structural integrity of diacylglycerol-depleted lipophorin was confirmed by electron microscopical analysis. When treated with both phospholipase A2 and triacylglycerol lipase, lipophorin precipitated. From these results we conclude that: 1) all phospholipid and apoLp-III are located at the surface of lipophorin, whereas diacylglycerol is partitioned between the sublayers and the surface of the particle; 2) both diacylglycerol and phospholipid play a role in stabilizing lipophorin in the aqueous medium; and 3) lipophorin can be extensively unloaded and still retain its basic structure, a necessary feature for its function as a reusable lipid shuttle.     

Intracellular pH distribution in Saccharomyces cerevisiae cell populations, analyzed by flow cytometry

Intracellular pH has an important role in the maintenance of the normal functions of yeast cells. The ability of the cell to maintain this pH homeostasis also in response to environmental changes has gained more and more interest in both basic and applied research. In this study we describe a protocol which allows the rapid determination of the intracellular pH of Saccharomyces cerevisiae cells. The method is based on flow cytometry and employs the pH-dependent fluorescent probe carboxy SNARF-4F. The protocol attempts to minimize the perturbation of the system under study, thus leading to accurate information about the physiological state of the single cell. Moreover, statistical analysis performed on major factors that may influence the final determination supported the validity of the optimized protocol. The protocol was used to investigate the effect of external pH on S. cerevisiae cells incubated in buffer. The results obtained showed that stationary cells are better able than exponentially grown cells to maintain their intracellular pH homeostasis independently of external pH changes. Furthermore, analysis of the intracellular pH distribution within the cell populations highlighted the presence of subpopulations characterized by different intracellular pH values. Notably, a different behavior was observed for exponentially grown and stationary cells in terms of the appearance and development of these subpopulations as a response to a changing external pH.     

Structure of Pseudomonas aeruginosa populations analyzed by single nucleotide polymorphism and pulsed-field gel electrophoresis genotyping

Pseudomonas aeruginosa has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of P. aeruginosa, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (oriC, oprL, fliC, alkB2, citS, oprI, and ampC). The combination of these SNPs plus the type of fliC present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of P. aeruginosa strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The P. aeruginosa chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the P. aeruginosa population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.     

利用InDel标记分析中国香菇菌株的遗传多样性与群体结构

通过对5个香菇菌株重测序,以香菇L808-1菌株的全基因组序列为参考基因组,分析了这些菌株中插入/缺失（InDel）标记位点在香菇基因组10条染色体上的分布,并筛选了插入/缺失碱基数≥15的位点,合成了449对InDel标记引物。经过PCR和电泳检测,其中237对引物条带清晰。最终筛选出107个PIC≥0.3的标记作为核心InDel标记对来自国内的44份香菇菌株进行遗传多样性分析。聚类分析显示栽培菌株和野生菌株各自聚为一支,所选香菇菌株间存在明显的群体分层。群体结构分析显示香菇种质资源可分为4个亚群,主成分分析显示香菇菌株之间的位置及距离与聚类分析和群体结构分析结果相符。香菇InDel分子标记的开发与应用,为香菇核心种质的构建和种质资源育种引用提供了基础。     

The interplay between microevolution and community structure in microbial populations

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Highlights► The action of industrial processes depends on microbial community structure. ► Microbes evolve very rapidly. ► Microbial evolution is affected by community structure. ► Community structure is affected by microbial evolution. ► This feedback may be crucial when considering microbial communities in industry.     

Genetic structure of Cydia pomonella populations in Argentina and Chile implies isolating barriers exist between populations

The codling moth (Cydia pomonella (L.)) is an invasive pest of pome fruits introduced to the Americas in the 19–20^th centuries. This pest is widespread on both sides of the Andes range separating Argentina and Chile. We performed an analysis of the population genetic variability and structure of C. pomonella in Argentina and Chile using 13 microsatellite markers and sampled C. pomonella from apple as the main host plant along its distribution area (approx. 1,800 km). A total of 22 locations (11 from Chile and 11 from Argentina) were sampled. Significant genetic differentiation was observed among samples from Argentina and Chile (F_SC = 0.045) and between all localities (F_ST = 0.085). Significant isolation by distance (IBD) was found for each country and when samples from both sides of the Andes range were pooled, although a lower correlation coefficient was observed. The Mantel test showed that the geographic distance and highest altitude of the mountains between locations were significantly associated with the pairwise F_ST when samples from both sides of the Andes range were pooled. According to a Bayesian assignment test (STRUCTURE), samples from Argentina and Chile conformed to two distinct genetic clusters. Our results also suggest that the recent invasion of C. pomonella in the southernmost localities (Aysén Region in Chile and Santa Cruz Province in Argentina) originated in populations from the respective sides of the Andes range. Our results indicate a genetic exchange of C. pomonella within each country and significant genetic differentiation between countries, which could be explained by dispersal mediated by human activities related to fruit production within each country with little exchange between them. A possible explanation is that the Andes range could be a significant barrier for dispersal by flight, and quarantine barriers could prevent the movement of plant material or infested fruit between countries.     

Evidence for nonrandom behavior in 208-12 subsaturated nucleosomal array populations analyzed by AFM

Atomic force microscopy was used to determine the population distributions in reconstituted, subsaturated 208-12 nucleosomal arrays. The features found in these distributions vary with the average nucleosome loading per template molecule (n(av)): at n(av) < 4, the distributions show a single peak whose breadth is equal to that expected for a random loading process; at n(av) = 4-8, the distributions are broader than random distributions and are complex; i.e., they contain multiple peaks and/or shoulders. Moreover, the peaks/shoulders typically occur at two nucleosome intervals, i.e., 2, 4, 6 or 3, 5, 7 nucleosomes. This two-nucleosome periodicity is statistically significant. The precise cause for such discrete features within the distributions is unknown, but at least these features would seem to indicate some pairwise preference in nucleosome occupation at these loading levels. In these intermediate-level (n(av) = 4-8) distributions, the major peak contains a larger fraction of the total templates than a random nucleosome loading process would produce. This feature indicates that at these intermediate population levels there is some tendency for correlated nucleosome loading among the templates. Hyperacetylated nucleosomal arrays show only subtle differences in their population distributions compared to nonacetylated arrays and demonstrate the above features. AFM allows one to study unfixed chromatin arrays; we find that nucleosomes on the 208-12 template demonstrate significant lability when they are not glutaraldehyde-fixed.     

Sicilian provinces: population subdivisions revealed by surname frequencies

The Sicilian population has a complex history of colonization and invasions that have influenced the genetic composition of the nine provinces of the island. Because surnames are patrilineally inherited, they simulate a Y-chromosome nonrecombinant genetic locus. We used surname data and a specific sampling strategy to describe the major subdivisions in each province and for the whole island of Sicily. The high number of families per surname in two provinces can be related to inbreeding as a result of founder events. Each province shows a major division, which, according to local historical events, likely represents cultural and probably genetic differences between east and west, between north and south, or between the inner regions and the coastal area. On the island level surnames reproduce the same separation, obtained by others with genes, of the eastern area from the western area. The separation is attributed to Greek influence in the east and to Phoenician-Carthaginian-Norman influence in the west. This separation crosses the two central provinces of Agrigento and Caltanissetta.     

Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography

Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)]₂. The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.     

Population structure of species: Eco-geographic units and genetic differentiation between populations

A two-step approach, based on a combined use of environmental, geographic, and genetic data, is suggested for studying population structures of species. First, populations are grouped into eco-geographic units (EGUs) according to the environmental gradients in the studied part of the species range, the types of life strategies, and other non-genetic characteristics that are presumably associated with adaptation and interpopulation gene flows. Second, the selected EGUs are tested for their congruence with genetic data by comparing the genetic differentiation between populations within EGUs to that between populations of different EGUs. Some of the issues discussed are as follows: the relationship of the EGU concept with the concepts of biogeocenosis and evolutionarily significant units (ESUs); designing EGUs in practice; the level of EGUs in a hierarchical population structure; and the weights of genetic and phenotypic markers in estimating population differentiation. The population structure of a salmonid fish, the Sakhalin taimen, in terms of eco-geographic units is considered as an example.