Phylogenetic reconstructions in the genus <Emphasis Type="Italic">Capra</Emphasis> (Bovidae,Artiodactyla) based on the mitochondrial DNA analysis

Mitochondrial genome fragments were examined in all species of the genus Capra (Bovidae, Artiodactyla). Phylogenetic analysis was carried out using 59 cytochrome b gene sequences (392 bp), and 22 sequences of the mtDNA variable fragment (402 bp). In the control region, two unique deletions were revealed. One of the deletions was found only in Capra cylindricornis (17 bp), while another one grouped C. caucasica with C. aegagrus (1 bp). The group of Caucasian wild goats splits into two clades, and furthermore, the sequences of C. caucasica demonstrate remarkable similarity to the sequences of C. aegagrus, while C. cylindricornis seems to have evolved independently for a long period of time. It was demonstrated that C. pyrenaica and C. ibex were extremely close to one another. Capra sibirica formed an outer group relative to the other species, and according to our data, was the most ancient species of the genus. On the contrary, genetic distance separating C. falconeri (the most independent species of the genus related to its morphology) from the other species is small.     

Ant–aphid relations in the south of Western Siberia (Hymenoptera: Formicidae; Hemiptera: Aphididae)

Aphids, the main suppliers of energy-rich honeydew, play an important role in the life of ants. However, the data on the trophobiotic ant–aphid associations in the majority of regions are still limited. We present the first data on the ant–aphid relations in the south of Western Siberia. Investigations were carried out in the most typical biotopes of forest-steppe and steppe zones in the territory of Novosibirsk and Kurgan regions (Russia) during 1993–2014. There were revealed 35 species of ants and 198 species of aphids. Detected 456 ant–aphid associations involved 28 ant species and 134 myrmecophilous aphids. Seven ant species were found to consume honeydew of 9 non-myrmecophilous aphids, scraping it from the plant. This behaviour is typical of subdominant and subordinate ants which do not protect their foraging areas. Ants associate with various numbers of aphid species. About 36% of ants attended aphid colonies of less than 5 species. The largest number of myrmecophilous aphids is associated with L. niger (Linnaeus, 1758) (103 species), Formica pratensis Retzius, 1783 (50), Formica rufa group (25–33), F. (Serviformica) fusca Linnaeus, 1758 (26) and F. (S.) cunicularia Latreille, 1798 (27). Different ants play unequal roles in the formation of trophobiotic interactions with aphids. Due to complex territorial and foraging behaviour, including high functional specialization among honeydew collectors, dominant ants of Formica s. str. are one of the leaders in this process. The role of L. niger and Formica ants of the subgenus Serviformica requires further detailed investigation.     

Phenotypic and phylogenetic characterization of actinomycetes isolated from <Emphasis Type="Italic">Lasius niger</Emphasis> and <Emphasis Type="Italic">Formica cunicularia</Emphasis> ants

Multiple actinomycete strains were isolated from two ant species, Lasius niger and Formica cunicularia, and their phenotypic properties and phylogenetic position were studied. Partial sequencing of 16S rRNA assigned the greater part of them to the genus Streptomyces, but only one belonged to Nocardia. However, some isolates had significant color and morphological differences from their closest phylogenetic relatives. The abundance and biodiversity of actinomycete communities isolated from L. niger ants greatly exceeded those found for F. cunicularia. All of the actinomycetes associated with F. cunicularia ants demonstrated cellulolytic activity, but only one had such ability among the strains associated with black ants.     

Mass Occurrence and Dominant Behavior of the European Ant Species <Emphasis Type="Italic">Formica fuscocinerea</Emphasis> (Forel)

Recently, masses of the ant Formica (Serviformica) fuscocinerea (Forel) have been occurring at numerous sites in Southern Germany. Although F. fuscocinerea is native to Southern Germany, these mass occurrences resemble ant invasions in density and dominance. This study aimed to investigate the underlying mechanisms that promote sudden mass occurrence of a previously inconspicuous ant species within its native range. To estimate the competitive dominance of F. fuscocinerea, species occurrence and abundance considering biotic and abiotic parameters were studied in a natural habitat where F. fuscocinerea co-occurred with two other common ant species, Myrmica ruginodis (Nylander) and Lasius niger (Linnaeus). To understand the species’ distribution in the field, laboratory experiments on interspecific competition were conducted. Finally, the colony structure of F. fuscocinerea was investigated with intraspecific aggression tests. Formica fuscocinerea dominated an area that, as indicated by strongly frequented foraging trails on the trees, provided important food sources, e.g. trophobionts, to the ants. Other ant species coexisted only at the periphery of the F. fuscocinerea range. Laboratory experiments revealed F. fuscocinerea as highly dominant species. Additionally, F. fuscocinerea showed a complete lack of intraspecific aggression between ants originating from distances up to 58 km, indicating weak or nonexistent behavioral boundaries among ants of physically separated nests. Since extraordinarily high worker densities, strong interspecific dominance and a lack of colony boundaries within supercolonies are considered to be important traits of several invasive ant species we conclude that the same traits also promote the dominance of F. fuscocinerea.     

Yeast communities of <Emphasis Type="Italic">Formica aquilonia</Emphasis> colonies

Yeast abundance and species diversity in the colonies of Formica aquilonia ants in birch–pine grass forest near Novosibirsk, Russia, were studied. The average yeast number in the anthill material was 10³–10⁴ CFU/g, reaching 10⁵ CFU/g in the hatching chambers. Typical litter species (Trichosporon moniliiforme and Cystofilobasidium capitatum) were predominant in soil and litter around the anthills. Apart from these species, ascomycete species of the family Debaryomycetaceae, Debaryomyces hansenii, and Schwanniomyces vanrijiae were predominant in the anthill material. Yeast population of the ant’ bodies consisted exclusively of the members of the last two species. Thus, highly specific yeast communities formed in the colonies of Formica aquilonia ants differ from the communities of surrounding soil. These differences are caused by environment-forming activity of the ants.     

Polymorphism and the secondary structure of the mitochondrial <Emphasis Type="Italic">nad1</Emphasis> gene b/c intron in <Emphasis Type="Italic">Malus</Emphasis> species and related Rosaceae species

Nucleotide sequences polymorphism of mitochondrial nad1 gene b/c intron was studied in 41 Malus accessions and 21 related Rosaceae accessions. The b/c intron sequence in genus Malus appeared to be very conservative, while in other studied Rosaceae species 126 variable sites and indels were detected in the intron sequence that varied in length from 1124 to 1456 bp. The predicted b/c intron pre-mRNA secondary structure for Malus species was determined; IBS/EBS binding sites and the boundaries of the six functional domains were identified.     

Effect of host species,host nest density and nest size on the occurrence of the shining guest ant <Emphasis Type="Italic">Formicoxenus nitidulus</Emphasis> (Hymenoptera: Formicidae)

Understanding habitat requirements of species is important in conservation. As an obligate ant nest associate, the survival of the globally vulnerable shining guest ant, Formicoxenus nitidulus, is strictly tied to that of its hosts (mound building Formica ants). We investigated how host species, nest density, inter-nest distance and nest mound size relate to the occurrence of F. nitidulus. In total, 166 red wood ant nests were surveyed in SW Finland (120 Formica polyctena, 25 F. rufa, 14 F. aquilonia, 5 F. pratensis, and 2 F. lugubris). Overall, F. nitidulus was found in 60% of the nests. For the actual analysis, only F. polyctena and F. rufa nests were included due to the small number of other nests. F. nitidulus was more likely to be found among F. polyctena than F. rufa. Also, while inter-nest distance was not important, a high nest density, commonly found in polydomous (multi-nest) wood ant colonies, was beneficial for F. nitidulus. The guest ant was also more likely to be found in large host nests than small nests. Thus, our results show that the best habitat for the guest ant is a dense population of host nest mounds with a high proportion of large mounds. Conservation efforts should be directed at keeping the quality of the red wood ant habitats high to preserve their current populations and to increase colonization. This will not only benefit the guest ant, but also a plethora of other species, and help in maintaining the biodiversity of forests.     

Genetic polymorphism,haplotype distribution,and phylogeny of <Emphasis Type="Italic">Daphnia</Emphasis> (Cladocera: Anomopoda) species from the water bodies of russia as inferred from the 16S mtDNA gene sequencing

The data on the genetic polymorphism of the most widespread Daphnia species occupying different water bodies of Russia are presented. The phylogenetic relationships between the examined species were established, and the haplotype networks were constructed. A fragment of the 16S mitochondrial DNA gene was used as a genetic marker. The results of molecular phylogenetic analysis generally coincided with modern concepts in the systematics of the genus Daphnia. The representatives of the divergent mitochondrial lineages within the D. longispina, D. pulex, and D. magna complex remain poorly investigated morphologically. For D. dentifera, a new habitat on the territory of Russia, namely, the water bodies of the Lake Baikal basin, was identified. A conclusion was made that the 16S mtDNA gene could be successfully used in phylogeographic analysis of the genus Daphnia.     

Larvae of the exotic predatory ladybird <Emphasis Type="Italic">Platynaspidius maculosus</Emphasis> (Coleoptera: Coccinellidae) on citrus trees: prey aphid species and behavioral interactions with aphid-attending ants in Japan

An aphidophagous ladybird, Platynaspidius maculosus (Weise) (Coleoptera: Coccinellidae), is originally distributed in China, Taiwan, and Vietnam. The ladybird has recently intruded into the southern and central parts of Japan. The present study found that the larvae of this ladybird preyed on three aphid species, Aphis spiraecola, Aphis gossypii, and Toxoptera citricidus (all Hemiptera: Aphididae), feeding on young shoots of various Citrus species in August to early October in Shizuoka Prefecture, central Japan. Laboratory rearing of the sampled larvae confirmed that the larvae completed their development (adult emergence) by consuming each of the three aphid species. The ladybird larvae were observed foraging in aphid colonies attended by one of the four ants, Lasius japonicus, Pristomyrmex punctatus, Formica japonica, and Camponotus japonicus (all Hymenoptera: Formicidae). Field observations revealed that the foraging/feeding larvae were almost completely ignored by honeydew-collecting ants even when they physically contacted each other. Thus, in Japan, the larvae of the exotic ladybird exploit colonies of the three aphid species attended by one of the four ant species on many Citrus species. On the basis of the results, I discuss the possibility of the ladybird’s reproduction on citrus trees in Japan, probable adaptations of the ladybird larvae to aphid-attending ants, and potential impacts of the ladybird on native insect enemies attacking ant-attended aphids on citrus.     

Contribution to the study of the genus <Emphasis Type="Italic">Lemniscomys</Emphasis> (Rodentia: Muridae). Morphometric and molecular approaches

A total of 204 specimens belonging to eight species of the genus Lemniscomys were examined with standard morphometric measurements. Our results show that the seven Sub-Saharan species seem to follow a latitudinal gradient from the Center to the South of the African continent. The only North African species L. barbarus looks close to L. griselda and L. rosalia. We also applied a molecular analysis through PCR (Polymerase Chain Reaction) method for the amplification of the 16S rRNA gene. For the purpose of constructing a phylogenetic tree with Maximum Likelihood method, we extracted eight sequences from the GenBank library; seven belonging to the genus Lemniscomys and one to the genus Arvicanthis used as outgroup. We managed to identify a region comprised of 458 nucleotides of which 388 were common for all species and 70 were variable. The phylogenetic tree shows us that the sister group L. bellieri and L. macculus, is the most basal, while L. striatus and L. rosalia appears to be close to the sister group L. barbarus and L. zebra. We also noticed a difference between morphometric and molecular results; the latter are more in agreement with pelage patterns subdivision between Lemniscomys species. These differences can be explained by a high rate of phenotypic evolution that can surpass the molecular counterpart as in the case of the genus Gerbillus.     

Retrotransposons in <Emphasis Type="Italic">Betula nana</Emphasis>, and interspecific relationships in the Betuloideae,based on inter-retrotransposon amplified polymorphism (IRAP) markers

The Betulaceae family comprises two subfamilies, Betuloideae and Corylaceae. The subfamily Betuloideae contains two genera, Alnus Mill. and Betula L. Twenty putative long terminal repeat (LTR) retrotransposons were mined from 171 scaffolds containing 5,208,995 bp of dwarf birch (Betula nana) genome sequences. Five retrotransposons were finally selected after filtering the retrotransposon canonical features and nucleotide similarities between left and right LTR sequences. Of the five retroelements, three elements were found to be Ty1/Copia retrotransposons; identity of the other two elements could not be ascertained due to sequence undetermined ‘N’ bases in the sequence database. Inter-retrotranposon amplified polymorphism (IRAP) analysis, based on the LTR sequences of the mined LTR-retrotransposons, produced 179 discernible IRAP bands among the Alnus and Betula genera. Sequence analysis revealed no size homoplasy among the homologous IRAP bands. Phylogenetic and principle coordinate analysis, based on the band sharing among the taxa, showed the species in two different genera were clearly separated. The subgenera in each genus of Alnus and Betula were also distinguishable from the IRAP profiles. In the genus Betula, the species in subgenus Betula showed mixed clustering between species. This is incongruent with the phylogeographical distribution of the species.     

A new species of the genus <Emphasis Type="Italic">Nalassus</Emphasis> Mulsant (Coleoptera: Tenebrionidae: Helopini) from the Baltic amber

The first Eocene species of the tribe Helopini, Nalassus klebsi sp. nov., from the Baltic amber is described. The new species is included in the nominative subgenus and similar to the extant species N. dermestoides (Illiger) and N. laevioctostriatus (Goeze), from which it differs in the shape of eyes (eyes are considerably less transverse than in living Palearctic species of the genus Nalassus Mulsant), the shape of the pronotum with acute posterior angles (other Palearctic Nalassus have obtuse or straight pronotal angles) as well as convex elytral intervals. Species of the less specialized nominative subgenus are widespread in forests and (partly) alpine landscapes of Europe (eastwards up to the Urals) and eastern Asia.     

Characterization,genetic diversity,phylogenetic relationships,and expression of the aluminum tolerance <Emphasis Type="Italic">MATE1</Emphasis> gene in <Emphasis Type="Italic">Secale</Emphasis> species

Aluminum (Al) is the main limiting factor for crop production in acidic soils. Efflux of organic acids is one of the mechanisms that determine Al-tolerance, and an Al-activated citrate transporter (multidrug and toxic compound extrusion) MATE1 gene is involved in different species. The contribution of the rye MATE1 gene (ScMATE1) depends on the rye (Secale cereale L.) cultivars and the crosses analyzed; there is no information about different rye species. The cDNA sequences, phylogenetic relationships, Al-tolerance, citrate exudation, and expression of the ScMATE1 gene were analyzed in several cultivars and wild species/subspecies of the Secale genus. Genotypes highly tolerant to Al were found within this genus. For the first time, sequences of the cDNA of the ScMATE1 gene were isolated and characterized in wild ryes. At least two copies of this gene were found likely to be related to Al-tolerance. The sequence comparison of 13 exons of ScMATE1 revealed variability between species, but also inter- and intra-cultivars. Variations were found in the Al-induced expression of ScMATE1 gene, as well as its contribution to Al-tolerance. The pattern of citrate exudation was inducible in most of the species/subspecies studied and constitutive in few. The phylogenetic analysis indicated that ScMATE1 is orthologue of two genes (HvMATE1 and TaMATE1) involved in the Al stress response in barley and wheat, respectively, but not orthologue of SbMATE, implicated in Al-tolerance in sorghum. ScMATE1 is involved in the response to Al stress in ryes, but its contribution to Al-tolerance is complex, and like in other species, there are tolerant and sensitive alleles in the different cultivars and species studied.     

Reduced ant defenses in <Emphasis Type="Italic">Macaranga</Emphasis> myrmecophytes (Euphorbiaceae) infested with a winged phasmid <Emphasis Type="Italic">Orthomeria cuprinus</Emphasis>

Macaranga is a tree genus that includes many species of myrmecophytes, which are plants that harbor ant colonies within hollow structures known as domatia. The symbiotic ants (plant–ants) protect their host plants against herbivores; this defense mechanism is called ‘ant defense’. A Bornean phasmid species Orthomeria cuprinus feeds on two myrmecophytic Macaranga species, Macaranga beccariana and Macaranga hypoleuca, which are obligately associated with Crematogaster ant species. The phasmids elude the ant defense using specialized behavior. However, the mechanisms used by the phasmid to overcome ant defenses have been insufficiently elucidated. We hypothesized that O. cuprinus only feeds on individual plants with weakened ant defenses. To test the hypothesis, we compared the ant defense intensity in phasmid-infested and non-infested M. beccariana trees. The number of plant–ants on the plant surface, the ratio of plant–ant biomass to tree biomass, and the aggressiveness of plant–ants towards experimentally introduced herbivores were significantly lower on the phasmid-infested trees than on the non-infested trees. The phasmid nymphs experimentally introduced into non-infested trees, compared with those experimentally introduced into phasmid-infested trees, were more active on the plant surface, avoiding the plant–ants. These results support the hypothesis and suggest that ant defenses on non-infested trees effectively prevent the phasmids from remaining on the plants. Thus, we suggest that O. cuprinus feeds only on the individual M. beccariana trees having decreased ant defenses, although the factors that reduce the intensity of the ant defenses remain unclear.     

Comparative analysis of complete chloroplast genome sequences of two subtropical trees, <Emphasis Type="Italic">Phoebe sheareri</Emphasis> and <Emphasis Type="Italic">Phoebe omeiensis</Emphasis> (Lauraceae)

Phoebe is an economically important genus from the family Lauraceae. It is widely distributed in tropical and subtropical Asia, but systematics of the genus is unclear, and currently there is no species-level phylogeny. Here, we determined the complete chloroplast genome sequences of two species with long-range PCR and next genome sequencing technologies, and identified mutation sites and highly variable regions. These highly variable sites were used to reconstruct the phylogeny. The plastomes of Phoebe sheareri and P. omeiensis were 152, 876, and 152, 855 bp, respectively. Comparative genomic analysis indicated that there are 222 mutation sites including 146 substitutions, 73 indels, and 3 microinversions in both plastomes. Fifty-six single-nucleotide changes were identified in gene-coding regions, and 45 microsatellite sites were found for use in species identification. Fourteen divergence hotspots of 38 variable regions were located. Phylogeny was reconstructed using a Bayesian and maximum likelihood approach for 12 Phoebe species and other five related Lauraceae based on 15 of the highly variable regions including accD-psaI, atpB-rbcL, ndhC-trnV, ndhF-rpl32, petA-psbJ, psaA, psbA-trnH, rbcL, rps8-rpl14, rps16-trnQ, rpl32-trnL, trnC-petN, trnL-trnF, trnS-trnG, and ycf1 indicated that variability in the chloroplast regions proposed as variable is enough to detect divergence events among 12 taxa of Phoebe, and that maybe also useful to help to elucidate further relationships among other taxa of the genus.     

On the taxonomic rank of <Emphasis Type="Italic">ciscaucasicus</Emphasis> and its relationships with the pygmy wood mouse <Emphasis Type="Italic">Sylvaemus uralensis</Emphasis> inferred from the mtDNA cytochrome b gene sequence

To specify the taxonomic rank of form ciscaucasicus (independent species Sylvaemus ciscaucasicus, or intraspecific form of pygmy wood mouse, S. uralensis), a 402-bp the mtDNA cytochrome b gene fragment (402 bp) was examined in ciscaucasicus individuals from six geographic localities of the Caucasus and Ciscaucasus (Krasnodar krai and Adygeya Republic) and 17 S. uralensis individuals from seven localities of the Russian Plain (Saratov oblast, Smolensk oblast, Voronezh oblast, Tula oblast, Moscow oblast, Tver’ oblast, and northern Krasnodar krai). For comparison, the cytochrome b gene was partly sequenced in the samples of yellow necked, S. flavicollis (n = 2, Samara oblast), and Caucasian, S. ponticus (n = 6, Krasnodar krai), wood mice. One Mus musculus specimen from Western Europe, whose nucleotide sequences were deposed in the GenBank, was used as intergeneric outgroup. Phylogenetic trees for the forms examined were constructed based on the mtDNA sequence variation and using the neighbor joining and maximum parsimony methods. The network of the cytochrome b haplotypes was also constructed. The level of genetic divergence was evaluated using Kimura’s two-parameter algorithm. Based on the data on the sequence variation in a 402-bp mtDNA cytochrome b gene fragment, the hypothesis on the species status of the ciscaucasicus form was. The mean intergroup distances (d) between the geographic groups of S. uralensis varied from 0.0036 to 0.0152. At the same time, the distances between the pygmy wood mice and the group of S. flavicollis-S. ponticus varies in the range from 0.0860 to 0.0935, and the level of intergeneric genetic differentiation (Sylvaemus-Mus) is higher than the latter index (d = 0.142). Ciscaucasicus should be considered as geographic substitution form of S. uralensis. Furthermore, the Caucasian populations of S. uralensis (= ciscaucasicus) were characterized by a threefold lower value of intergroup genetic divergence (d = 0.0062) than the East European populations (d = 0.0179). This finding pointed to some isolation of Caucasian populations of pygmy wood mouse and depletion of their gene pool. However other molecular genetic data (similarity of nucleotide composition and consistence of the levels of intra-and intergroup distances) suggest the absence of geographic subdivision between Caucasian and East European populations of S. uralensis relative to the molecular marker examined.     

Structure of the <Emphasis Type="Italic">TADHN</Emphasis> gene for dehydrin-like protein of soft wheat and activation of its expression by ABA and 24-epibrassinolide

The structure of the cloned fragment of wheat (Triticum aestivum L.) TADHN gene encoding dehydrin-like protein was examined. A comparative analysis of nucleotide and deduced amino acid sequences revealed a high homology of this fragment with sequences of the barley dhn8 gene and wheat wcor gene family. In deduced amino acid sequence of the TADHN fragment, a 15-residue region EKKGFLEKIKEKLPG was found, which corresponded to a highly conserved K-segment of dehydrins. Wheat seedling treatment with 3.7 μM ABA and 0.4 μM 24-epibrassinolide exerted similar stimulatory effects on expression of the TADHN gene, which indicates the involvement of dehydrins in the protective action of these phytohormones in wheat plants.