Life Cycles of Ground Beetles (Coleoptera,Carabidae) from the Mountain Taiga and Mountain Forest-Steppe in the Eastern Sayan

Seasonal dynamics and demographic structure was studied in 15 dominant ground beetle species in the mountain taiga and mountain forest-steppe belts of the Eastern Sayan (Okinskoe Plateau). Life cycles of the dominant ground beetle species were classified by developmental time, seasonal dynamics, and intrapopulation groups with different reproduction timing. The strategies of carabid life cycles adapted to severe mountain conditions of the Eastern Sayan were revealed.     

Features of the life cycles of <Emphasis Type="Italic">Pterostichus montanus</Emphasis> (Motschulsky, 1844) and <Emphasis Type="Italic">Carabus loschnikovi</Emphasis> (Fischer-Waldheim, 1822) (Coleoptera,Carabidae) in conditions of the mountain taiga belt in the Eastern Sayan

We studied the seasonal dynamics and demographic structure of abundant ground beetle species from the mountain taiga belt in the Eastern Sayan. Data on the dynamics of the sexual and age structure of the populations as well as on the reproductive capacity of females in the biotopes on the slopes with different exposure and height were obtained. Life cycles with one-and two-year development were revealed for the ground beetles typical for the mountain taiga belt. As an example, data on the life cycles of Pterostichus montanus (Motschulsky, 1844) with one-year spring development and Carabus loschnikovi (Fischer-Waldheim, 1822) with two-year polyvariant multiseasonal development are given for the first time. Two strategies were revealed in the life cycles of ground beetles under alpine conditions: an accelerated population development in spring one-year species and a two-year development with pronounced polyvariance in two intrapopulation groups of ground beetles of the Carabus genus. The seasonal dynamics of the activity and reproduction periods proved to vary for these species on the slopes along the height gradient.Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 1, 2005, pp. 36–46.Original Russian Text Copyright © 2005 by Sharova, Khobrakova.     

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Background

Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F_ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.

Results

Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F_ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F_ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F_ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.

Conclusions

Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-876) contains supplementary material, which is available to authorized users.     

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

Background

Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns.

Methods

By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation.

Results

For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1.

Conclusions

The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.     

Altitudinal variation of the life cycle of Poecilus fortipes (Coleoptera,Carabidae) in Eastern Siberia

Altitudinal variation of the demographic structure of populations of Poecilus fortipes (Chaud.) was studied in four mountain localities in the south of Eastern Siberia, and the life cycle of the species was reconstructed for each locality. The size of adults of both sexes decreased along the altitudinal gradient: the beetles from the Selenga middle mountains (600–650 m above sea level) were much larger, while those at the upper boundary of the forest-steppe belt in the Eastern Sayan (1500–1700 m asl) were smaller than others. Their linear dimensions decreased more distinctly in the transitional zone between middle and high mountains. The duration of the reproductive period did not depend on the altitude. However, the onset of oviposition shifted along the altitudinal gradient to the beginning of the vegetation season, due to its shortening and a decrease in the sum of effective temperatures. As the altitude increased, the mean number of eggs per female declined significantly from 15.9 ± 6.1 to 8.6 ± 5.8, whereas the maximum number of eggs increased from 26–28 to 40–43. On the contrary, the dates of emergence shifted gradually from the beginning and middle of the vegetation period to its middle and end. Populations from the Selenga middle mountains, the Vitim Plateau, and the lower margin of the forest-steppe belt in the Eastern Sayan mountains were characterized by a relatively low catch index and the absence of rebreeding old individuals, both these features increasing the risk of spontaneous local extinction. The annual life cycle with summer breeding was replaced along the altitudinal gradient with an obligate biennial life cycle with summer and early-summer breeding. This transition was observed as the altitude increased from 600–650 to 900–950 m asl while the sum of effective temperatures dropped below 1400°C, i.e., the value needed for implementation of the annual life cycle.     

Impact of temperature on Na2Sr(PO4)F:Eu3+ phosphor

In this article, we report the synthesis of Na₂Sr_1‐x(PO₄)F:Eu_x phosphor via a combustion method. The influence of different annealing temperatures on the photoluminescence properties was investigated. The phosphor was excited at both 254 and 393 nm. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors emit strong orange and red color at 593 and 612 nm, respectively, under both excitation wavelengths. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors annealed at 1050°C showed stronger emission intensity compared with 600, 900 and 1200°C. Moreover, Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphor was found to be more intense when compared with commercial Y₂O₃:Eu³⁺ phosphor. Copyright © 2013 John Wiley & Sons, Ltd.     

Ground-beetle (Coleoptera,Carabidae) assemblages in the forest-steppe of the southern Vitim Plateau

A list of species and the structure of ground beetle assemblages in the forest-steppe of Eravninskaya (= Sosnovoozerskaya) Depression situated in the permafrost area are presented. Ground beetle assemblages dwelling in larch, mixed, and small-leaved forests (intact and after fires), and also in the meadow steppe and waterlogged meadows with varying degrees of humidity were studied. The data obtained demonstrate that the communities examined are intermediate between those revealed in adjacent territories of the Selenga River basin, mid-altitude mountains, and of the northern Transbaikalia. The gentle sauce-shaped relief of Eravninskaya Depression is responsible for the concentric circular distribution of carabid assemblages, occasionally interrupted by forest-steppe fragments in isolated forests and meadow steppes. All the hill slopes surrounding the depression are populated by taiga carabid assemblages, whereas the bottom of the depression is the habitat for meadow-steppe and forest-steppe assemblages.     

Symmetric cyanine dyes for detecting nucleic acids

A novel approach to the design of sensitive fluorescent probes for nucleic acids detection is proposed. Suitable modifications of tri- and pentamethine cyanine dyes in the polymethine chain and/or in the heterocyclic residues can result in a significant decrease in unbound dye fluorescence intensity and an increase in dye emission intensity in the presence of DNA compared to the unsubstituted dye. The sharp enhancement in the fluorescence intensity upon dye interaction with double-stranded DNA permits the application of the modified tri- and pentamethine dyes as fluorescent probes in double-stranded DNA detection in homogeneous assays.     

M31R and R335C polymorphic variants of the IL8RA gene in Russian and Buryat patients with atopic bronchial asthma

To test the M31R and R335C polymorphisms of the Il8RA gene for association with atopic bronchial asthma (BA), the allele and genotype frequency distributions of the polymorphisms were studied in Russian patients from Moscow and Buryat patients from Ulan-Ude. The study involved two Russian groups, one including 291 DNA samples of patients with atopic BA, and the other, 266 DNA samples of healthy people. The two Buryat groups included 124 and 152 DNA samples from patients with atopic BA and healthy people, respectively. The M31R polymorphism proved to be associated with atopic BA in Russians. Allele Arg and genotype Met/Arg suggested a higher risk of BA (OR= 4.45, P = 0.003 and OR = 4.58, P = 0.003, respectively), while allele Met and genotype Met/Metwere associated with a lower risk (OR = 0.22, P = 0.003 and OR = 0.22, P = 0.003, respectively). The R335C polymorphism was not associated with atopic BA in Russians and was in Buryats. Allele Arg and homozygous genotype Arg/Arg suggested a higher risk of the disease (OR = 3.06, P = 0.030 and OR = 3.20, P = 0.027, respectively), while allele Cys and genotype Arg/Cys suggested a lower risk (OR = 0.33, P = 0.030 and OR = 0.31, P = 0.027, respectively). The results support the role of the IL8RA gene in atopic BA.     

Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations

Background

Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds.

Results

We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings.

Conclusions

The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0109-5) contains supplementary material, which is available to authorized users.