Wolbachia, Spiroplasma, and Rickettsia symbiotic bacteria in aphids (Aphidoidea).

Aphids are a diverse family of crop pests. Aphids formed a complex relationship with intracellular bacteria. Depending on the region of study, the species composition of both aphids and their facultative endosymbionts varies. The aim of the work was to determine the occurrence and genetic diversity of Wolbachia, Spiroplasma and Rickettsia symbionts in aphids collected in 2018-2019 in Moscow. For these purposes, 578 aphids from 32 collection sites were tested by PCR using specific primers. At least 21 species of aphids from 14 genera and four families were identified by barcoding method, of which 11 species were infected with endosymbionts. Rickettsia was found in six species, Wolbachia in two species, Spiroplasma in one species. The presence of Rickettsia in Impatientinum asiaticum, Myzus cerasi, Hyalopterus pruni, Eucallipterus tiliae, Chaitophorus tremulae and Wolbachia in Aphis pomi and C. tremulae has been described for the first time. A double infection with Rickettsia and Spiroplasma was detected in a half of pea aphid (Acyrthosiphon pisum) individuals. For the first time was found that six species of aphids are infected with Rickettsia that are genetically different from previously known. It was first discovered that A. pomi is infected with two Wolbachia strains, one of which belongs to supergroup B and is genetically close to Wolbachia from C. tremulae. The second Wolbachia strain from A. pomi belongs to the supergroup M, recently described in aphid species. Spiroplasma, which we observed in A. pisum, is genetically close to male killing Spiroplasma from aphids, ladybirds and moths. Both maternal inheritance and horizontal transmission are the pathways for the distribution of facultative endosymbiotic bacteria in aphids.

[Horizontal gene transfer into the genomes of insects].

Horizontal gene transfer (HGT) is widespread in the world of prokaryotes, but the examples of this phenomenon among multicellular animals, particularly insects, are few. This review examines the transfer of genetic material to the nuclear genomes of insects from the mitochondrial genome (intracellular HGT), as well as from the genomes of viruses, bacteria, fungi, and unrelated insects. In most cases, the mechanisms of this transfer are unknown. Many pro- and eukaryotic genes that moved through the HGT are expressed in the insect genome and in some cases can provide the evolutionary innovations that are considered as aromorphoses.

[Genotypic Diversity of Wolbachia pipientis in Native and Invasive Harmonia axyridis Pall., 1773 (Coleoptera, Coccinellidae) Populations].

The distribution and variability of reproductive symbiotic Wolbachia pipientis bacteria were studied in seven native and six invasive H. axyridis populations. Wolbachia-infected individuals were found in two invasive and two native populations. We demonstrated for the first time an infection of invasive H. axyridis populations with Wolbachia. Two new molecular forms of Wolbachia were detected by a system of multilocus typing. The supergroup A Wolbachia was found for the first time in H. axyridis. The detected genotypic diversity of Wolbachia indicates repeated and independent infection events in the evolutionary past of H. axyridis.

[Identification of potentially invasive species of black flies [Diptera: Simuliidae] from Armenia based on an analysis of variability in the mtDNA barcode of the cox1 gene and chromosomal polymorphism].

Black flies (Diptera, Simuliidae) are well known for their medical, environmental, and veterinary importance. The simuliid fauna of Armenia includes 53 species. A number of dominant species are of ecological importance. Complex analysis, which involved morphometric, cytogenetic, and molecular genetic approaches, was conducted to characterize the species status of black flies inhabiting the territory of Armenia. It was shown that the predominant simuliid species, Simulium paraequinum and Simulium kiritshenkoi, belong to a group of species with minimal variability of the cox1 gene. The recently discovered species, Simulium noellery and Simulium [B.] erythrocephalum, which are new to Armenia, can be considered as potentially invasive, which is supported by the low level of variability of the cox1 gene.

[Coevolution of symbiotic bacteria Wolbachia and host mtDNA in Russian populations of the Culex pipiens mosquito complex].

The mitochondrial DNA phylogenies of closely related forms of mosquitoes from the Culex pipiens complex and of strains of the endosymbiotic bacteria Wolbachia pipientis were compared. Based on the cytochrome oxidase subunit I gene polymorphism, six mitochondrial haplotypes and four W. pipientis groups were discovered in mosquitoes from geographically remote populations. A strict correlation between the COI type and the type of W. pipientis proves the stable coinheritance and distribution of both cytoplasmic components in the examined mosquito populations and suggests either the absence or rarity of horizontal transfer of the symbionts in the Culex pipiens complex.

Investigating the genetic load of an emblematic invasive species: the case of the invasive harlequin ladybird Harmonia axyridis.

Introduction events can lead to admixture between genetically differentiated populations and bottlenecks in population size. These processes can alter the adaptive potential of invasive species by shaping genetic variation, but more importantly, they can also directly affect mean population fitness either increasing it or decreasing it. Which outcome is observed depends on the structure of the genetic load of the species. The ladybird Harmonia axyridis is a good example of invasive species where introduced populations have gone through admixture and bottleneck events. We used laboratory experiments to manipulate the relatedness among H. axyridis parental individuals to assess the possibility for heterosis or outbreeding depression in F1 generation offspring for two traits related to fitness (lifetime performance and generation time). We found that inter-populations crosses had no major impact on the lifetime performance of the offspring produced by individuals from either native or invasive populations. Significant outbreeding depression was observed only for crosses between native populations for generation time. The absence of observed heterosis is indicative of a low occurrence of fixed deleterious mutations within both the native and invasive populations of H. axyridis. The observed deterioration of fitness in native inter-population crosses most likely results from genetic incompatibilities between native genomic backgrounds. We discuss the implications of these results for the structure of genetic load in H. axyridis in the light of the available information regarding the introduction history of this species.

[Polymorphism of mitochondrial DNA and distribution of cytoplasmic symbionts in the populations of two-spot ladybird beetle Adalia bipunctata].

In geographically distant populations of ladybird beetle Adalia bipunctata from Eurasia mitotypes and infection with symbiotic bacteria Spiroplasma and Rickettsia were determined. All populations examined demonstrated mtDNA polymorphism and striking differences in prevalence of bacteria (from about 50% of individuals infected with Spiroplasma in St.-Petersburg population and 50% of the Rickettsia prevalence in Kem' population to complete absence of bacteria in the population from Archangelsk). In the populations studied a total of 14 mitotypes were discovered, including two mitotypes that were remarkably different from the others in nucleotide composition. Mitotype 10, which was the most different from all the others, was found in all populations from Germany to Transbaikalia, excluding the population from Tashkent. Linkage disequilibrium between mitotype 10 and the Rickettsia infection was confirmed. Infection with the Spiroplasma bacteria was typical of the individuals with haplotype 1 and relative to it. The results obtained supported the conclusion on the association between infection with Spiroplasma and Rickettsia and certain mitotype of A. bipunctata, which was the consequence of either absence or rare horizontal transfer of symbionts and ancientness of the first contact between the bacteria and A. bipunctata ladybird beetles.

Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis.

Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that native area of H. axyridis most probably consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete and (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.

[A search for a "Genghis Khan chromosome"].

Zerial et al. (2003) have shown that a special variant of the Y chromosome, characterized by a set of microsatellite markers occurs at high frequency in the number of human populations of Central Asia. This variant was attributed to the descendants of Genghis Khan and its accumulation, to social selection. A search of this Y chromosome variant in Russian populations was conducted. The "Genghis Khan Y chromosome" has been found among Altaians, Altai Kazakhs, Buryats, Kalmyks, Nogaits, and Tuvinians. Its highest frequency (13.8%) was observed in Nogaits. In the examined cases the carriers of the "Genghis Khan Y chromosome" possessed no information on their origin.

[Location of genes in chromosomes: random or not?].

The possibility is discussed that the order of genes in chromosomes is not random but determined by natural selection, i.e., is a selectively valuable character. Cases of long-term conservation of gene linkage or synteny in evolution are presented. Examples and possible mechanisms of nonrandom gene localization in prokaryotic and eukaryotic chromosomes are considered.

[Genetic polymorphism of Microbotryum violaceum s. I. isolates collected from different plant species on the territory of Russia].

The present-day studies in the field of systematics and phylogeny of microorganisms, fungi, in particular, are characterized by a wide use of new approaches and methods of molecular biology. The use of a diversity of genetic markers permits a distinct differentiation of closely related species into individual evolutionary independent lines. It is shown in this work that all Microbotryum violaceum s. l. isolates studied by us are divided into five evolutionary groups according to the host plant.

[Evolution of gene orders in genomes of cyanobacteria].

Genomes of 23 strains of cyanobacteria were comparatively analyzed using quantitative methods of estimation of gene order similarity. It has been found that reconstructions of phylogenesis of cyanobacteria based on the comparison of the orders of genes in chromosomes and nucleotide sequences appear to be similar. This confirms the applicability of quantitative measures of similarity of gene orders for phylogenetic reconstructions. In the evolution of marine unicellular plankton cyanobacteria, genome rearrangements are fixed with a low rate (about 3% of gene order changes per 1% of 16S rRNA changes), whereas in other groups of cyanobacteria the gene order can change several times more rapidly. The gene orders in genomes of cyanobacteria and chloroplasts preserve a considerable degree of similarity. The closest relatives of chloroplasts among the analyzed cyanobacteria are likely to be strains from hot springs belonging to the genus Synechococcus. Comparative analysis of gene orders and nucleotide sequences strongly suggests that Synechococcus strains from diferent environments (sea, fresh waters, hot springs) are not related and belong to evolutionally distant lines.

[Evolution of gene orders in mycoplasmas (Bacteria, Firmicutes, Mollicutes)].

Quantitative methods of estimation of similarity between gene orders have been used to compare the genomes of 14 strains of mycoplasmas and 2 strains of phytoplasmas, i.e., all genomes of bacteria of the class Mollicutes deciphered to date. Reconstructions of the mycoplasma phylogeny based on comparisons of (a) gene orders in a chromosome and (b) nucleotide or amino acid sequences have proved to be almost identical, which confirms that quantitative measures of gene order similarity can be used for meaningful phylogenetic reconstructions. Genomic rearrangements have been almost equally frequent in the evolutions of three main groups of mycoplasmas. A gene order changes by 1% approximately every 7 Myr or less (the calculation is based on the assumption that a 1% change in the nucleotide sequence of the 16S rRNA gene requires, on average, 50 Myr). In contrast to another analyzed group of obligately parasitic bacteria (rickettsiae), no distinct tendency towards a decrease in the rate of genomic rearrangements has been found in the evolution of mycoplasmas.

[Use of quantitative measures of gene order similarity to phylogenetic reconstructions (exemplified by bacteria of the genus Rickettsia)].

Data reflecting evolutionary changes in chromosomal gene order can be used for phylogenetic reconstructions along with the results of nucleotide sequence comparison. By the example of bacteria of the genus Rickettsia, we have shown that phylogenetic reconstructions based on quantitative estimates of the similarity and cladistic analysis of gene order data, may, in some cases, amend and fill up classical phylogenetic trees. When applied, these approaches enabled us to substantiate the hypothesis that Rickettsia felis species had split before the typhus (R. typhi, R. prowazekii) and spotted fever (R. connorii) group divergence and thus R. felis does not belong to the latter group. In general, rickettsias evolved towards increasing intracellular parasitic specialization. Five Rickettsia species whose genomes have been sequenced and annotated completely actually form an evolutionary series R. hellii-R. felis-R. connorii-R. prowazekii-R. typhi. Within this series, a reduction in genome size and rapid decrease of genome rearrangement rates (genome plasticity loss) gradually occur.

[Removing endosymbiotic Wolbachia specifically decreases lifespan of females and competitiveness in a laboratory strain of Drosophila melanogaster].

To understand specific symbiotic relationships ensuring stable existing of the bacterium Wolbachia in laboratory strains of Drosophila melanogaster, the imago lifespan and senescence rate, as well as competitiveness, have been evaluated as components of fitness in females from the following laboratory strains: (1) inbred strain 95 infected with Wolbachia; (2) two uninfected strains obtained by tetracycline treatment that were genetically similar to strain 95; and (3) two control, uninfected, wild-type laboratory strains that were used to assess the possible effects of the antibiotic on the studied characters in the absence of Wolbachia. The results have shown that infected females have longer lifespan and competitiveness than females with the same genotype uninfected with Wolbachia. The increase in the senescence and mortality rates with age was also slower in infected females. It is noteworthy that tetracycline does not affect the lifespan of females from the two control, uninfected, wild-type strains. Therefore, the antibiotic is not the cause of the positive changes in fitness that were observed in infected females. The obtained results are the first direct evidence that the relationship s in the Wolbachia-D melanogaster symbiotic system are mutualistic rather than parasitic, at least in micropopulations adapted to laboratory conditions.

[Variability of fifteen autosomal microsatellite DNA loci in five populations of aboriginal South Siberians].

The allele distributions for 15 STR loci included in the AmpFISTR SGM Plus and AmpFISTR Profiler Plus kits ("Applied Biosystems", USA) were determined in 261 healthy unrelated individuals belonging to five indigenous populations of South Siberia: in Buryats, Altaians, Tofalars, Sojots and Khakassians. No significant differences in allele frequencies were found between populations studied. Combined power of discrimination (PD) for the STR loci investigated were estimated for the populations under study.

[Distribution of the male lineages of Genghis Khan's descendants in northern Eurasian populations].

Data on the variation of 12 microsatellite loci of Y-chromosome haplogroup C3 were used to screen lineages included in the cluster of Genghis Khan's descendants in 18 northern Eurasian populations (Altaian Kazakhs, Altaians-Kizhi, Teleuts, Khakassians, Shorians, Tyvans, Todjins, Tofalars, Sojots, Buryats, Khamnigans, Evenks, Mongols, Kalmyks, Tajiks, Kurds, Persians, and Russians; the total sample size was 1437 people). The highest frequency of haplotypes from the cluster of the Genghis Khan's descendants was found in Mongols (34.8%). In Russia, this cluster was found in Altaian Kazakhs (8.3%), Altaians (3.4%), Buryats (2.3%), Tyvans (1.9%), and Kalmyks (1.7%).

Inheritance of litter size at birth in farmed arctic foxes (Alopex lagopus, Canidae, Carnivora).

Natural populations of the arctic fox (Alopex lagopus, Canidae, Carnivora) differ drastically in their reproductive strategy. Coastal foxes, which depend on stable food resources, produce litters of moderate size. Inland foxes feed on small rodents, whose populations are characterized by cycling fluctuation. In the years with low food supply, inland fox populations have a very low rate of reproduction. In the years with high food supply, they undergo a population explosion. To gain insight into the genetic basis of the reproductive strategy of this species, we performed complex segregation analysis of the litter size in the extended pedigree of the farmed arctic foxes involving 20,665 interrelated animals. Complex segregation analysis was performed using a mixed model assuming that the trait was under control of a major gene and a large number of additive genetic and random factors. To check the significance of any major gene effect, we used Elston-Stewart transmission probability test. Our analysis demonstrated that the inheritance of this trait can be described within the frameworks of a major gene model with recessive control of low litter size. This model was also supported by the pattern of its familial segregation and by comparison of the distributions observed in the population and that expected under our model. We suggest that a system of balanced polymorphism for litter size in the farmed population might have been established in natural populations of arctic foxes as a result of adaptation to the drastic fluctuations in prey availability.

[Large and small rearrangements in the evolution of prokaryotic genomes].

Relative frequencies of large and small genome rearrangements (inversions and transpositions) in the evolution of prokaryotic genomes can be evaluated using the ratio between the index S (the ratio of the number of identical pairs of neighboring genes in two genomes to the total number of genes in the sample of interest) and 1 - 6 x L/n, where L is the mean difference in intergenic distances and n is the number of genes in the sample. The S value uniformly decreases with the fixation of genome rearrangements, while the decrease rate of I - 6 x L/n is determined by the rearrangement size. Specifically, large inversions and transpositions lead to a dramatic decrease in the index value, while small rearrangements result in an insignificant decrease. The ratio between these indices was computed for twenty pairs of closely related species belonging to different groups of bacteria and archaea. The pairs examined strongly differed in the relative frequency of large and small rearrangements. However, computer simulation showed that the total variation can be reproduced with the same input parameters of the model. This means that the differences observed can be stochastic and can be interpreted without assuming different mechanisms and factors of genome rearrangements for different groups of prokaryotes. Relative frequencies of large and small rearrangements displayed no noticeable correlations with taxonomic position, total rate of rearrangement fixation, habitation conditions, and the abundance of transposons and repetitive sequences. It is suggested that, in some cases, phage activity increases the frequency of large genome rearrangements.